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PDBsum entry 3rfy

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Isomerase PDB id
3rfy
Jmol
Contents
Protein chain
356 a.a.
Waters ×114
HEADER    ISOMERASE                               07-APR-11   3RFY
TITLE     CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA CYCLOPHILIN 38 (ATCYP38)
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE CYP38, CHLOROPLASTIC;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: PPIASE CYP38, ROTAMASE CYP38, THYLAKOID LUMEN PPIASE;
COMPND   5 EC: 5.2.1.8;
COMPND   6 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA;
SOURCE   3 ORGANISM_COMMON: MOUSE-EAR CRESS,THALE-CRESS;
SOURCE   4 ORGANISM_TAXID: 3702;
SOURCE   5 GENE: AT3G01480, CYP38, F4P13.3;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3);
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: PGEX-KG
KEYWDS    CYCLOPHILIN, CYP38, PEPTIDYL PROLYL ISOMERASE, PPIASE, TLP, ISOMERASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    D.VASUDEVAN,K.SWAMINATHAN
REVDAT   3   16-OCT-13 3RFY    1       JRNL
REVDAT   2   27-JUN-12 3RFY    1       JRNL
REVDAT   1   13-JUN-12 3RFY    0
JRNL        AUTH   D.VASUDEVAN,A.FU,S.LUAN,K.SWAMINATHAN
JRNL        TITL   CRYSTAL STRUCTURE OF ARABIDOPSIS CYCLOPHILIN38 REVEALS A
JRNL        TITL 2 PREVIOUSLY UNCHARACTERIZED IMMUNOPHILIN FOLD AND A POSSIBLE
JRNL        TITL 3 AUTOINHIBITORY MECHANISM.
JRNL        REF    PLANT CELL                    V.  24  2666 2012
JRNL        REFN                   ISSN 1040-4651
JRNL        PMID   22706283
JRNL        DOI    10.1105/TPC.111.093781
REMARK   2
REMARK   2 RESOLUTION.    2.39 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : CNS 1.1
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK   3               : READ,RICE,SIMONSON,WARREN
REMARK   3
REMARK   3  REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.39
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 19.89
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 3188772.680
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 0.0000
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 86.9
REMARK   3   NUMBER OF REFLECTIONS             : 16411
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
REMARK   3   R VALUE            (WORKING SET) : 0.248
REMARK   3   FREE R VALUE                     : 0.266
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.900
REMARK   3   FREE R VALUE TEST SET COUNT      : 669
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 0.010
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : 6
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.39
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.54
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 55.80
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 1642
REMARK   3   BIN R VALUE           (WORKING SET) : 0.3440
REMARK   3   BIN FREE R VALUE                    : 0.3150
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 5.20
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 90
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.033
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 2765
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 0
REMARK   3   SOLVENT ATOMS            : 114
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 43.40
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 69.10
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : 6.49000
REMARK   3    B22 (A**2) : -3.78000
REMARK   3    B33 (A**2) : -2.71000
REMARK   3    B12 (A**2) : 0.00000
REMARK   3    B13 (A**2) : 0.00000
REMARK   3    B23 (A**2) : 0.00000
REMARK   3
REMARK   3  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.36
REMARK   3   ESD FROM SIGMAA              (A) : 0.32
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 5.00
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 0.37
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.27
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : 0.016
REMARK   3   BOND ANGLES            (DEGREES) : 2.90
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 27.20
REMARK   3   IMPROPER ANGLES        (DEGREES) : 2.17
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND              (A**2) : 2.160 ; 1.500
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : 3.680 ; 2.000
REMARK   3   SIDE-CHAIN BOND              (A**2) : 4.050 ; 2.000
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : 5.240 ; 2.500
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED : FLAT MODEL
REMARK   3   KSOL        : 0.36
REMARK   3   BSOL        : 67.63
REMARK   3
REMARK   3  NCS MODEL : NULL
REMARK   3
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  PARAMETER FILE  1  : PROTEIN_REP.PARAM
REMARK   3  PARAMETER FILE  2  : WATER_REP.PARAM
REMARK   3  PARAMETER FILE  3  : NULL
REMARK   3  TOPOLOGY FILE  1   : PROTEIN.TOP
REMARK   3  TOPOLOGY FILE  2   : WATER.TOP
REMARK   3  TOPOLOGY FILE  3   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK   3  POSITIONS
REMARK   4
REMARK   4 3RFY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-APR-11.
REMARK 100 THE RCSB ID CODE IS RCSB064882.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 09-JUN-06
REMARK 200  TEMPERATURE           (KELVIN) : 103
REMARK 200  PH                             : 5.5
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : NSLS
REMARK 200  BEAMLINE                       : X12C
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9797, 0.9794, 0.9500
REMARK 200  MONOCHROMATOR                  : DOUBLE-CRYSTAL MONOCHROMATOR
REMARK 200                                   SI(111)
REMARK 200  OPTICS                         : VERTICALLY COLLIMATING MIRROR
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 210
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 19441
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.390
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 98.6
REMARK 200  DATA REDUNDANCY                : 6.400
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : 0.06700
REMARK 200   FOR THE DATA SET  : 19.2100
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.55
REMARK 200  COMPLETENESS FOR SHELL     (%) : 91.6
REMARK 200  DATA REDUNDANCY IN SHELL       : 4.30
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : 0.23000
REMARK 200   FOR SHELL         : 5.100
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: MAD
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: BNP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 57.98
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 6000, 2.5% T-BUTANOL, 100MM
REMARK 280  SODIUM CITRATE (PH 5.5), VAPOR BATCH, TEMPERATURE 293K, VAPOR
REMARK 280  DIFFUSION
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,-Y,Z+1/2
REMARK 290       3555   -X,Y,-Z+1/2
REMARK 290       4555   X,-Y,-Z
REMARK 290       5555   X+1/2,Y+1/2,Z
REMARK 290       6555   -X+1/2,-Y+1/2,Z+1/2
REMARK 290       7555   -X+1/2,Y+1/2,-Z+1/2
REMARK 290       8555   X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290     WHERE NNN -> OPERATOR NUMBER
REMARK 290           MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       83.41000
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       83.41000
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   5  1.000000  0.000000  0.000000       28.84500
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       48.36000
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   6 -1.000000  0.000000  0.000000       28.84500
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       48.36000
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000       83.41000
REMARK 290   SMTRY1   7 -1.000000  0.000000  0.000000       28.84500
REMARK 290   SMTRY2   7  0.000000  1.000000  0.000000       48.36000
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000       83.41000
REMARK 290   SMTRY1   8  1.000000  0.000000  0.000000       28.84500
REMARK 290   SMTRY2   8  0.000000 -1.000000  0.000000       48.36000
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000        0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3490 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 41790 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   2  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   2  0.000000 -1.000000  0.000000       96.72000
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000      166.82000
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375      HOH A 682  LIES ON A SPECIAL POSITION.
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465   M RES C SSSEQI
REMARK 465     GLY A    69
REMARK 465     SER A    70
REMARK 465     PRO A    71
REMARK 465     GLY A    72
REMARK 465     ILE A    73
REMARK 465     SER A    74
REMARK 465     GLY A    75
REMARK 465     GLY A    76
REMARK 465     GLY A    77
REMARK 465     LYS A   434
REMARK 465     ILE A   435
REMARK 465     ALA A   436
REMARK 465     GLY A   437
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE
REMARK 500   N    LEU A   125     O    HOH A   671              1.98
REMARK 500   OE1  GLU A   426     O    HOH A   654              2.03
REMARK 500   OG   SER A   380     O    HOH A   641              2.04
REMARK 500   OE1  GLU A   426     O    HOH A   605              2.04
REMARK 500   O    ALA A   200     N    LYS A   202              2.11
REMARK 500   O    GLU A   287     O    PRO A   350              2.13
REMARK 500   O    LEU A   154     N    GLN A   156              2.14
REMARK 500   O    GLN A   122     O    PRO A   124              2.16
REMARK 500   OD1  ASP A   300     O    HOH A   610              2.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT.  AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500.  ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI  SSYMOP   DISTANCE
REMARK 500   O    HOH A   605     O    HOH A   605     3555     2.15
REMARK 500   O    TRP A   375     O    HOH A   602     4566     2.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500  M RES CSSEQI ATM1   RES CSSEQI ATM2   DEVIATION
REMARK 500    TRP A 375   NE1   TRP A 375   CE2     0.124
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3
REMARK 500    LEU A  81   N   -  CA  -  C   ANGL. DEV. =  17.3 DEGREES
REMARK 500    PRO A  86   C   -  N   -  CA  ANGL. DEV. = -10.4 DEGREES
REMARK 500    PRO A  89   C   -  N   -  CA  ANGL. DEV. =  19.0 DEGREES
REMARK 500    PRO A  89   C   -  N   -  CD  ANGL. DEV. = -15.0 DEGREES
REMARK 500    PRO A 124   C   -  N   -  CA  ANGL. DEV. = -13.6 DEGREES
REMARK 500    GLY A 164   N   -  CA  -  C   ANGL. DEV. =  19.1 DEGREES
REMARK 500    PHE A 165   N   -  CA  -  C   ANGL. DEV. =  17.5 DEGREES
REMARK 500    VAL A 191   N   -  CA  -  C   ANGL. DEV. = -17.2 DEGREES
REMARK 500    ARG A 194   N   -  CA  -  C   ANGL. DEV. = -20.5 DEGREES
REMARK 500    PRO A 201   C   -  N   -  CA  ANGL. DEV. = -17.2 DEGREES
REMARK 500    LYS A 202   N   -  CA  -  C   ANGL. DEV. = -18.6 DEGREES
REMARK 500    PRO A 222   C   -  N   -  CD  ANGL. DEV. = -15.1 DEGREES
REMARK 500    GLN A 297   N   -  CA  -  C   ANGL. DEV. = -23.3 DEGREES
REMARK 500    THR A 298   N   -  CA  -  C   ANGL. DEV. =  17.6 DEGREES
REMARK 500    VAL A 319   N   -  CA  -  C   ANGL. DEV. = -16.6 DEGREES
REMARK 500    ASP A 367   N   -  CA  -  C   ANGL. DEV. =  17.1 DEGREES
REMARK 500    GLN A 372   N   -  CA  -  C   ANGL. DEV. =  20.3 DEGREES
REMARK 500    TRP A 375   CD2 -  CE2 -  CZ2 ANGL. DEV. =   9.4 DEGREES
REMARK 500    TRP A 375   CE2 -  CD2 -  CG  ANGL. DEV. =   7.7 DEGREES
REMARK 500    ASN A 388   N   -  CA  -  C   ANGL. DEV. =  18.6 DEGREES
REMARK 500    LEU A 390   CA  -  CB  -  CG  ANGL. DEV. =  17.7 DEGREES
REMARK 500    ASP A 391   N   -  CA  -  C   ANGL. DEV. =  19.7 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500  M RES CSSEQI        PSI       PHI
REMARK 500    VAL A  87      -24.03     66.76
REMARK 500    ASP A  90      -15.69     89.69
REMARK 500    PRO A 124     -151.37    -67.30
REMARK 500    LEU A 125      -53.26     63.14
REMARK 500    VAL A 137      -18.39    -35.32
REMARK 500    GLN A 155       86.84    -52.88
REMARK 500    GLN A 156       29.25    166.47
REMARK 500    ILE A 161      -72.46    -65.58
REMARK 500    VAL A 162      -92.90    -62.69
REMARK 500    ALA A 163      -74.62     -4.75
REMARK 500    ALA A 166      137.29     68.14
REMARK 500    GLU A 167     -105.00      5.71
REMARK 500    LYS A 189       92.45    -63.71
REMARK 500    ILE A 190       34.28    170.72
REMARK 500    ASP A 193      124.48    -23.57
REMARK 500    ARG A 194     -179.15     95.69
REMARK 500    ALA A 198       26.31    -70.48
REMARK 500    VAL A 199      -33.80   -161.32
REMARK 500    ALA A 200      -70.46    -49.67
REMARK 500    PRO A 201       57.32    -66.29
REMARK 500    MET A 217     -119.77    -70.59
REMARK 500    ASP A 219     -154.40   -115.92
REMARK 500    PHE A 221      172.20     51.44
REMARK 500    PRO A 222      104.50     17.09
REMARK 500    GLU A 224     -141.67   -126.14
REMARK 500    ARG A 230       15.01    -65.32
REMARK 500    ASN A 252       86.69     82.46
REMARK 500    ILE A 253      110.90     93.78
REMARK 500    ARG A 280       23.37    -74.10
REMARK 500    SER A 291     -178.72    178.64
REMARK 500    ASP A 300      -77.91   -137.12
REMARK 500    GLU A 302     -141.63   -110.21
REMARK 500    PRO A 304      137.45    -32.87
REMARK 500    ILE A 309      -80.26   -123.60
REMARK 500    GLU A 314      109.39    141.32
REMARK 500    LYS A 315      132.14    136.81
REMARK 500    ARG A 317     -146.17     62.63
REMARK 500    PRO A 320      -98.74    -67.05
REMARK 500    GLU A 322      -88.50   -166.85
REMARK 500    ILE A 323       18.52    102.73
REMARK 500    MET A 324      159.10     33.91
REMARK 500    VAL A 325     -178.05    -12.36
REMARK 500    THR A 326      -78.59    -60.25
REMARK 500    LYS A 329     -102.46    144.80
REMARK 500    THR A 330      131.93     37.25
REMARK 500    PRO A 331      118.55    -24.50
REMARK 500    PHE A 332     -170.60      8.11
REMARK 500    TYR A 333      108.80    169.87
REMARK 500    SER A 335      -27.99    172.28
REMARK 500    PHE A 351       94.44    120.75
REMARK 500
REMARK 500 THIS ENTRY HAS      72 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500  M RES CSSEQI    IMPROPER   EXPECTED   FOUND DETAILS
REMARK 500    PHE A 165        22.3      L          L   OUTSIDE RANGE
REMARK 500    ALA A 166        24.3      L          L   OUTSIDE RANGE
REMARK 500    GLU A 227        24.5      L          L   OUTSIDE RANGE
REMARK 500    PRO A 251        46.4      L          L   OUTSIDE RANGE
REMARK 500    GLN A 297        47.3      L          L   OUTSIDE RANGE
REMARK 500    THR A 298        24.2      L          L   OUTSIDE RANGE
REMARK 500    ASP A 300        24.0      L          L   OUTSIDE RANGE
REMARK 500    MET A 324        24.5      L          L   OUTSIDE RANGE
REMARK 500    VAL A 325        22.6      L          L   OUTSIDE RANGE
REMARK 500    LYS A 329        21.0      L          L   OUTSIDE RANGE
REMARK 500    ASN A 352        25.0      L          L   OUTSIDE RANGE
REMARK 500    ASP A 367        22.6      L          L   OUTSIDE RANGE
REMARK 500    GLN A 372        21.0      L          L   OUTSIDE RANGE
REMARK 500    PHE A 374        23.5      L          L   OUTSIDE RANGE
REMARK 500    SER A 387        24.5      L          L   OUTSIDE RANGE
REMARK 500    ASN A 388        23.4      L          L   OUTSIDE RANGE
REMARK 500    ASP A 391        20.8      L          L   OUTSIDE RANGE
REMARK 500    ARG A 393        24.8      L          L   OUTSIDE RANGE
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525  M RES CSSEQI
REMARK 525    HOH A 620        DISTANCE =  5.59 ANGSTROMS
REMARK 525    HOH A 626        DISTANCE =  6.15 ANGSTROMS
REMARK 525    HOH A 677        DISTANCE =  5.31 ANGSTROMS
REMARK 525    HOH A 678        DISTANCE =  9.59 ANGSTROMS
DBREF  3RFY A   83   437  UNP    Q9SSA5   CYP38_ARATH     83    437
SEQADV 3RFY GLY A   69  UNP  Q9SSA5              EXPRESSION TAG
SEQADV 3RFY SER A   70  UNP  Q9SSA5              EXPRESSION TAG
SEQADV 3RFY PRO A   71  UNP  Q9SSA5              EXPRESSION TAG
SEQADV 3RFY GLY A   72  UNP  Q9SSA5              EXPRESSION TAG
SEQADV 3RFY ILE A   73  UNP  Q9SSA5              EXPRESSION TAG
SEQADV 3RFY SER A   74  UNP  Q9SSA5              EXPRESSION TAG
SEQADV 3RFY GLY A   75  UNP  Q9SSA5              EXPRESSION TAG
SEQADV 3RFY GLY A   76  UNP  Q9SSA5              EXPRESSION TAG
SEQADV 3RFY GLY A   77  UNP  Q9SSA5              EXPRESSION TAG
SEQADV 3RFY GLY A   78  UNP  Q9SSA5              EXPRESSION TAG
SEQADV 3RFY GLY A   79  UNP  Q9SSA5              EXPRESSION TAG
SEQADV 3RFY ILE A   80  UNP  Q9SSA5              EXPRESSION TAG
SEQADV 3RFY LEU A   81  UNP  Q9SSA5              EXPRESSION TAG
SEQADV 3RFY LEU A   82  UNP  Q9SSA5              EXPRESSION TAG
SEQRES   1 A  369  GLY SER PRO GLY ILE SER GLY GLY GLY GLY GLY ILE LEU
SEQRES   2 A  369  LEU VAL ALA ASN PRO VAL ILE PRO ASP VAL SER VAL LEU
SEQRES   3 A  369  ILE SER GLY PRO PRO ILE LYS ASP PRO GLU ALA LEU LEU
SEQRES   4 A  369  ARG TYR ALA LEU PRO ILE ASP ASN LYS ALA ILE ARG GLU
SEQRES   5 A  369  VAL GLN LYS PRO LEU GLU ASP ILE THR ASP SER LEU LYS
SEQRES   6 A  369  ILE ALA GLY VAL LYS ALA LEU ASP SER VAL GLU ARG ASN
SEQRES   7 A  369  VAL ARG GLN ALA SER ARG THR LEU GLN GLN GLY LYS SER
SEQRES   8 A  369  ILE ILE VAL ALA GLY PHE ALA GLU SER LYS LYS ASP HIS
SEQRES   9 A  369  GLY ASN GLU MET ILE GLU LYS LEU GLU ALA GLY MET GLN
SEQRES  10 A  369  ASP MET LEU LYS ILE VAL GLU ASP ARG LYS ARG ASP ALA
SEQRES  11 A  369  VAL ALA PRO LYS GLN LYS GLU ILE LEU LYS TYR VAL GLY
SEQRES  12 A  369  GLY ILE GLU GLU ASP MET VAL ASP GLY PHE PRO TYR GLU
SEQRES  13 A  369  VAL PRO GLU GLU TYR ARG ASN MET PRO LEU LEU LYS GLY
SEQRES  14 A  369  ARG ALA SER VAL ASP MET LYS VAL LYS ILE LYS ASP ASN
SEQRES  15 A  369  PRO ASN ILE GLU ASP CYS VAL PHE ARG ILE VAL LEU ASP
SEQRES  16 A  369  GLY TYR ASN ALA PRO VAL THR ALA GLY ASN PHE VAL ASP
SEQRES  17 A  369  LEU VAL GLU ARG HIS PHE TYR ASP GLY MET GLU ILE GLN
SEQRES  18 A  369  ARG SER ASP GLY PHE VAL VAL GLN THR GLY ASP PRO GLU
SEQRES  19 A  369  GLY PRO ALA GLU GLY PHE ILE ASP PRO SER THR GLU LYS
SEQRES  20 A  369  THR ARG THR VAL PRO LEU GLU ILE MET VAL THR GLY GLU
SEQRES  21 A  369  LYS THR PRO PHE TYR GLY SER THR LEU GLU GLU LEU GLY
SEQRES  22 A  369  LEU TYR LYS ALA GLN VAL VAL ILE PRO PHE ASN ALA PHE
SEQRES  23 A  369  GLY THR MET ALA MET ALA ARG GLU GLU PHE GLU ASN ASP
SEQRES  24 A  369  SER GLY SER SER GLN VAL PHE TRP LEU LEU LYS GLU SER
SEQRES  25 A  369  GLU LEU THR PRO SER ASN SER ASN ILE LEU ASP GLY ARG
SEQRES  26 A  369  TYR ALA VAL PHE GLY TYR VAL THR ASP ASN GLU ASP PHE
SEQRES  27 A  369  LEU ALA ASP LEU LYS VAL GLY ASP VAL ILE GLU SER ILE
SEQRES  28 A  369  GLN VAL VAL SER GLY LEU GLU ASN LEU ALA ASN PRO SER
SEQRES  29 A  369  TYR LYS ILE ALA GLY
FORMUL   2  HOH   *114(H2 O)
HELIX    1   1 ASP A  102  LEU A  111  1                                  10
HELIX    2   2 ASN A  115  ASP A  127  1                                  13
HELIX    3   3 ASP A  127  LEU A  132  1                                   6
HELIX    4   4 ALA A  139  GLN A  155  1                                  17
HELIX    5   5 GLN A  156  VAL A  162  1                                   7
HELIX    6   6 ALA A  166  SER A  168  5                                   3
HELIX    7   7 LYS A  169  LYS A  189  1                                  21
HELIX    8   8 VAL A  199  PRO A  201  5                                   3
HELIX    9   9 LYS A  202  MET A  217  1                                  16
HELIX   10  10 ALA A  267  ARG A  280  1                                  14
HELIX   11  11 LEU A  337  LEU A  340  5                                   4
HELIX   12  12 ASP A  405  LEU A  410  5                                   6
HELIX   13  13 GLY A  424  GLU A  426  5                                   3
SHEET    1   A11 MET A 286  GLU A 287  0
SHEET    2   A11 VAL A 415  SER A 423 -1  O  ILE A 416   N  MET A 286
SHEET    3   A11 ARG A 238  LYS A 246 -1  N  SER A 240   O  VAL A 422
SHEET    4   A11 ASP A 255  ASP A 263 -1  O  PHE A 258   N  MET A 243
SHEET    5   A11 TYR A 394  ASP A 402 -1  O  PHE A 397   N  ASP A 263
SHEET    6   A11 LYS A 378  LEU A 382  1  N  SER A 380   O  TYR A 394
SHEET    7   A11 GLN A 289  VAL A 296  1  N  PHE A 294   O  GLU A 379
SHEET    8   A11 LEU A 342  ILE A 349 -1  O  VAL A 347   N  SER A 291
SHEET    9   A11 VAL A  93  SER A  96 -1  N  SER A  96   O  GLN A 346
SHEET   10   A11 ILE A  80  ALA A  84 -1  N  LEU A  81   O  ILE A  95
SHEET   11   A11 TYR A 394  ASP A 402 -1  O  ALA A 395   N  ALA A  84
SHEET    1   B 2 LEU A 234  LEU A 235  0
SHEET    2   B 2 LEU A 428  ALA A 429 -1  O  ALA A 429   N  LEU A 234
CRYST1   57.690   96.720  166.820  90.00  90.00  90.00 C 2 2 21      8
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.017334  0.000000  0.000000        0.00000
SCALE2      0.000000  0.010339  0.000000        0.00000
SCALE3      0.000000  0.000000  0.005994        0.00000
      
PROCHECK
Go to PROCHECK summary
 References