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PDBsum entry 1xc8

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Top Page protein dna_rna ligands metals links
Hydrolase/DNA PDB id
1xc8
Jmol
Contents
Protein chain
271 a.a.
DNA/RNA
Ligands
GOL
Metals
_ZN
Waters ×397
HEADER    HYDROLASE/DNA                           01-SEP-04   1XC8
TITLE     CRYSTAL STRUCTURE COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG
TITLE    2 (MUTM) AND A FAPY-DG CONTAINING DNA
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: 5'-D(*CP*TP*CP*TP*TP*TP*(FOX)P*TP*TP*TP*CP*TP*CP*G)-3';
COMPND   3 CHAIN: B;
COMPND   4 ENGINEERED: YES;
COMPND   5 MOL_ID: 2;
COMPND   6 MOLECULE: 5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3';
COMPND   7 CHAIN: C;
COMPND   8 ENGINEERED: YES;
COMPND   9 MOL_ID: 3;
COMPND  10 MOLECULE: FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE;
COMPND  11 CHAIN: A;
COMPND  12 SYNONYM: FAPY-DNA GLYCOSYLASE;
COMPND  13 EC: 3.2.2.23;
COMPND  14 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 SYNTHETIC: YES;
SOURCE   3 MOL_ID: 2;
SOURCE   4 SYNTHETIC: YES;
SOURCE   5 MOL_ID: 3;
SOURCE   6 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS SUBSP. CREMORIS;
SOURCE   7 ORGANISM_TAXID: 1359;
SOURCE   8 STRAIN: SUBSP. CREMORIS;
SOURCE   9 VARIANT: SUBSP. CREMORIS;
SOURCE  10 GENE: MUTM, FPG;
SOURCE  11 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE  12 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE  13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE  14 EXPRESSION_SYSTEM_PLASMID: PMAL-C
KEYWDS    PROTEIN-DNA COMPLEX; GLYCOSYLASE; FAPY, HYDROLASE-DNA COMPLEX
EXPDTA    X-RAY DIFFRACTION
AUTHOR    F.COSTE,M.OBER,T.CARELL,S.BOITEUX,C.ZELWER,B.CASTAING
REVDAT   3   13-JUL-11 1XC8    1       VERSN
REVDAT   2   24-FEB-09 1XC8    1       VERSN
REVDAT   1   06-SEP-05 1XC8    0
JRNL        AUTH   F.COSTE,M.OBER,T.CARELL,S.BOITEUX,C.ZELWER,B.CASTAING
JRNL        TITL   STRUCTURAL BASIS FOR THE RECOGNITION OF THE FAPYDG LESION
JRNL        TITL 2 (2,6-DIAMINO-4-HYDROXY-5-FORMAMIDOPYRIMIDINE) BY
JRNL        TITL 3 FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE.
JRNL        REF    J.BIOL.CHEM.                  V. 279 44074 2004
JRNL        REFN                   ISSN 0021-9258
JRNL        PMID   15249553
JRNL        DOI    10.1074/JBC.M405928200
REMARK   2
REMARK   2 RESOLUTION.    1.95 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5.2
REMARK   3   AUTHORS     : MURSHUDOV,VAGIN,DODSON
REMARK   3
REMARK   3    REFINEMENT TARGET : NULL
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 17.25
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : 90.9
REMARK   3   NUMBER OF REFLECTIONS             : 39561
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 + TEST SET) : 0.178
REMARK   3   R VALUE            (WORKING SET) : 0.176
REMARK   3   FREE R VALUE                     : 0.209
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.000
REMARK   3   FREE R VALUE TEST SET COUNT      : 2089
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : 20
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 1.95
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.00
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 2920
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 93.25
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2130
REMARK   3   BIN FREE R VALUE SET COUNT          : 148
REMARK   3   BIN FREE R VALUE                    : 0.2330
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 2128
REMARK   3   NUCLEIC ACID ATOMS       : 569
REMARK   3   HETEROGEN ATOMS          : 7
REMARK   3   SOLVENT ATOMS            : 397
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 35.41
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : 0.33000
REMARK   3    B22 (A**2) : 0.33000
REMARK   3    B33 (A**2) : -0.67000
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 OVERALL COORDINATE ERROR.
REMARK   3   ESU BASED ON R VALUE                            (A): 0.122
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.120
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.073
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.496
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.963
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.950
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  2808 ; 0.020 ; 0.022
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  3900 ; 1.776 ; 2.239
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   270 ; 5.971 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):    86 ;35.416 ;23.953
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   413 ;11.965 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    12 ;17.948 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   442 ; 0.119 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  1852 ; 0.008 ; 0.020
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  1173 ; 0.211 ; 0.200
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  1844 ; 0.303 ; 0.200
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):   306 ; 0.161 ; 0.200
REMARK   3   H-BOND (X...Y) OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION REFINED ATOMS (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):    28 ; 0.133 ; 0.200
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):    16 ; 0.207 ; 0.200
REMARK   3   SYMMETRY H-BOND OTHERS            (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY METAL-ION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY METAL-ION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.     COUNT   RMS    WEIGHT
REMARK   3   MAIN-CHAIN BOND REFINED ATOMS  (A**2):  1420 ; 1.223 ; 1.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  2168 ; 1.745 ; 2.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1776 ; 2.727 ; 3.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  1732 ; 3.962 ; 4.500
REMARK   3
REMARK   3 ANISOTROPIC THERMAL FACTOR RESTRAINTS.    COUNT   RMS   WEIGHT
REMARK   3   RIGID-BOND RESTRAINTS          (A**2):  NULL ;  NULL ;  NULL
REMARK   3   SPHERICITY; FREE ATOMS         (A**2):  NULL ;  NULL ;  NULL
REMARK   3   SPHERICITY; BONDED ATOMS       (A**2):  NULL ;  NULL ;  NULL
REMARK   3
REMARK   3  NCS RESTRAINTS STATISTICS
REMARK   3   NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK   3
REMARK   3  TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  : NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELLING.
REMARK   3   METHOD USED : BABINET MODEL WITH MASK
REMARK   3   PARAMETERS FOR MASK CALCULATION
REMARK   3   VDW PROBE RADIUS   : 1.20
REMARK   3   ION PROBE RADIUS   : 0.80
REMARK   3   SHRINKAGE RADIUS   : 0.80
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 1XC8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-04.
REMARK 100 THE RCSB ID CODE IS RCSB030194.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 11-JUL-04
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 7.0
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : ESRF
REMARK 200  BEAMLINE                       : BM30A
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.92004
REMARK 200  MONOCHROMATOR                  : DOUBLE CRYSTAL MONOCHROMATOR
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : MARRESEARCH
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XNEMO
REMARK 200  DATA SCALING SOFTWARE          : CCP4 (SCALA)
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 41650
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.950
REMARK 200  RESOLUTION RANGE LOW       (A) : 17.247
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 91.4
REMARK 200  DATA REDUNDANCY                : NULL
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : 0.06900
REMARK 200   FOR THE DATA SET  : 7.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.06
REMARK 200  COMPLETENESS FOR SHELL     (%) : 91.4
REMARK 200  DATA REDUNDANCY IN SHELL       : 4.80
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : 0.28400
REMARK 200   FOR SHELL         : 2.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: PDB ENTRY 1TDZ
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 64.80
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.52
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, SODIUM CITRATE, PH 7.0, VAPOR
REMARK 280  DIFFUSION, HANGING DROP, TEMPERATURE 303K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2
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   -Y+1/2,X+1/2,Z+1/4
REMARK 290       4555   Y+1/2,-X+1/2,Z+3/4
REMARK 290       5555   -X+1/2,Y+1/2,-Z+1/4
REMARK 290       6555   X+1/2,-Y+1/2,-Z+3/4
REMARK 290       7555   Y,X,-Z
REMARK 290       8555   -Y,-X,-Z+1/2
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       71.43350
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       46.25650
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       46.25650
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       35.71675
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       46.25650
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       46.25650
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000      107.15025
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       46.25650
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       46.25650
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       35.71675
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       46.25650
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       46.25650
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000      107.15025
REMARK 290   SMTRY1   7  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY2   7  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   8  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY2   8 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000       71.43350
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
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: TRIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 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 A5294  LIES ON A SPECIAL POSITION.
REMARK 375      HOH A5216  LIES ON A SPECIAL POSITION.
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470   M RES CSSEQI  ATOMS
REMARK 470     LYS A  15    CD   CE   NZ
REMARK 470     ARG A  31    CZ   NH1  NH2
REMARK 470     LYS A  42    CD   CE   NZ
REMARK 470     ASP A  65    CG   OD1  OD2
REMARK 470     ASP A  66    CG   OD1  OD2
REMARK 470     LYS A  78    CD   CE   NZ
REMARK 470     ARG A  88    CG   CD   NE   CZ   NH1  NH2
REMARK 470     ASP A 100    CG   OD1  OD2
REMARK 470     GLN A 121    CD   OE1  NE2
REMARK 470     LYS A 130    CE   NZ
REMARK 470     GLU A 138    CG   CD   OE1  OE2
REMARK 470     ARG A 150    CD   NE   CZ   NH1  NH2
REMARK 470     LYS A 187    NZ
REMARK 470     GLN A 191    CD   OE1  NE2
REMARK 470     LYS A 213    CG   CD   CE   NZ
REMARK 470     ARG A 220    CG   CD   NE   CZ   NH1  NH2
REMARK 470     LYS A 230    CE   NZ
REMARK 470     LYS A 271    CE   NZ
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   OP2   DA C    22     O    HOH C   372              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     DT B   8   C5     DT B   8   C7      0.039
REMARK 500    CYS A 265   CB    CYS A 265   SG      0.108
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     DT B   2   O4' -  C1' -  N1  ANGL. DEV. =   1.9 DEGREES
REMARK 500     DT B   6   O4' -  C1' -  N1  ANGL. DEV. =   1.9 DEGREES
REMARK 500     DT B   6   C4  -  C5  -  C7  ANGL. DEV. =   4.3 DEGREES
REMARK 500     DT B   8   O4' -  C1' -  N1  ANGL. DEV. =  -4.4 DEGREES
REMARK 500     DT B  12   C5  -  C4  -  O4  ANGL. DEV. =  -4.5 DEGREES
REMARK 500     DC B  13   O4' -  C1' -  C2' ANGL. DEV. =  -5.2 DEGREES
REMARK 500     DC B  13   O4' -  C1' -  N1  ANGL. DEV. =  -4.7 DEGREES
REMARK 500     DG C  15   O4' -  C1' -  N9  ANGL. DEV. =   3.9 DEGREES
REMARK 500     DG C  17   O5' -  C5' -  C4' ANGL. DEV. =  -6.0 DEGREES
REMARK 500     DA C  18   O4' -  C1' -  N9  ANGL. DEV. =  -4.6 DEGREES
REMARK 500     DA C  20   O4' -  C1' -  N9  ANGL. DEV. =   4.6 DEGREES
REMARK 500     DC C  23   O5' -  P   -  OP2 ANGL. DEV. =  -6.1 DEGREES
REMARK 500     DC C  23   O4' -  C4' -  C3' ANGL. DEV. =  -2.4 DEGREES
REMARK 500     DC C  23   C1' -  O4' -  C4' ANGL. DEV. =  -6.4 DEGREES
REMARK 500     DG C  27   O4' -  C1' -  N9  ANGL. DEV. =   4.2 DEGREES
REMARK 500     DA C  28   O4' -  C1' -  N9  ANGL. DEV. =   4.5 DEGREES
REMARK 500    LEU A  40   CA  -  CB  -  CG  ANGL. DEV. =  18.4 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    ARG A  74     -124.15     45.58
REMARK 500    VAL A 166      143.03   -170.83
REMARK 500    ARG A 220      -42.44   -133.14
REMARK 500    VAL A 237      -37.90   -134.30
REMARK 500    GLN A 269       76.27   -118.98
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 A5154        DISTANCE =  5.24 ANGSTROMS
REMARK 525    HOH A5190        DISTANCE =  5.05 ANGSTROMS
REMARK 525    HOH A5268        DISTANCE =  6.13 ANGSTROMS
REMARK 525    HOH A5309        DISTANCE =  5.14 ANGSTROMS
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              ZN A5001  ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 268   SG
REMARK 620 2 CYS A 248   SG  115.5
REMARK 620 3 CYS A 265   SG  112.7  95.8
REMARK 620 4 CYS A 245   SG  107.0 113.1 112.8
REMARK 620 N                    1     2     3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 5001
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1001
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1TDZ   RELATED DB: PDB
REMARK 900 MUTANT ENZYME
DBREF  1XC8 A    1   271  UNP    P42371   FPG_LACLC        2    273
DBREF  1XC8 B    1    14  PDB    1XC8     1XC8             1     14
DBREF  1XC8 C   15    28  PDB    1XC8     1XC8            15     28
SEQADV 1XC8     A       UNP  P42371    ASP   139 DELETION
SEQRES   1 B   14   DC  DT  DC  DT  DT  DT FOX  DT  DT  DT  DC  DT  DC
SEQRES   2 B   14   DG
SEQRES   1 C   14   DG  DC  DG  DA  DG  DA  DA  DA  DC  DA  DA  DA  DG
SEQRES   2 C   14   DA
SEQRES   1 A  271  PRO GLU LEU PRO GLU VAL GLU THR VAL ARG ARG GLU LEU
SEQRES   2 A  271  GLU LYS ARG ILE VAL GLY GLN LYS ILE ILE SER ILE GLU
SEQRES   3 A  271  ALA THR TYR PRO ARG MET VAL LEU THR GLY PHE GLU GLN
SEQRES   4 A  271  LEU LYS LYS GLU LEU THR GLY LYS THR ILE GLN GLY ILE
SEQRES   5 A  271  SER ARG ARG GLY LYS TYR LEU ILE PHE GLU ILE GLY ASP
SEQRES   6 A  271  ASP PHE ARG LEU ILE SER HIS LEU ARG MET GLU GLY LYS
SEQRES   7 A  271  TYR ARG LEU ALA THR LEU ASP ALA PRO ARG GLU LYS HIS
SEQRES   8 A  271  ASP HIS LEU THR MET LYS PHE ALA ASP GLY GLN LEU ILE
SEQRES   9 A  271  TYR ALA ASP VAL ARG LYS PHE GLY THR TRP GLU LEU ILE
SEQRES  10 A  271  SER THR ASP GLN VAL LEU PRO TYR PHE LEU LYS LYS LYS
SEQRES  11 A  271  ILE GLY PRO GLU PRO THR TYR GLU ASP PHE ASP GLU LYS
SEQRES  12 A  271  LEU PHE ARG GLU LYS LEU ARG LYS SER THR LYS LYS ILE
SEQRES  13 A  271  LYS PRO TYR LEU LEU GLU GLN THR LEU VAL ALA GLY LEU
SEQRES  14 A  271  GLY ASN ILE TYR VAL ASP GLU VAL LEU TRP LEU ALA LYS
SEQRES  15 A  271  ILE HIS PRO GLU LYS GLU THR ASN GLN LEU ILE GLU SER
SEQRES  16 A  271  SER ILE HIS LEU LEU HIS ASP SER ILE ILE GLU ILE LEU
SEQRES  17 A  271  GLN LYS ALA ILE LYS LEU GLY GLY SER SER ILE ARG THR
SEQRES  18 A  271  TYR SER ALA LEU GLY SER THR GLY LYS MET GLN ASN GLU
SEQRES  19 A  271  LEU GLN VAL TYR GLY LYS THR GLY GLU LYS CYS SER ARG
SEQRES  20 A  271  CYS GLY ALA GLU ILE GLN LYS ILE LYS VAL ALA GLY ARG
SEQRES  21 A  271  GLY THR HIS PHE CYS PRO VAL CYS GLN GLN LYS
MODRES 1XC8 FOX B    7   DG
HET    FOX  B   7      23
HET     ZN  A5001       1
HET    GOL  A1001       6
HETNAM     FOX ((1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-3,6-
HETNAM   2 FOX  DIHYDROPYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL)
HETNAM   3 FOX  METHYL 5'-PHOSPHATE
HETNAM      ZN ZINC ION
HETNAM     GOL GLYCEROL
HETSYN     GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL   1  FOX    C11 H18 N5 O7 P
FORMUL   4   ZN    ZN 2+
FORMUL   5  GOL    C3 H8 O3
FORMUL   6  HOH   *397(H2 O)
HELIX    1   1 GLU A    2  VAL A   18  1                                  17
HELIX    2   2 TYR A   29  VAL A   33  5                                   5
HELIX    3   3 GLY A   36  THR A   45  1                                  10
HELIX    4   4 GLN A  121  LYS A  130  1                                  10
HELIX    5   5 ASP A  141  LYS A  151  1                                  11
HELIX    6   6 LYS A  155  GLU A  162  1                                   8
HELIX    7   7 GLY A  170  ALA A  181  1                                  12
HELIX    8   8 GLU A  188  LEU A  192  5                                   5
HELIX    9   9 ILE A  193  LEU A  214  1                                  22
HELIX   10  10 LYS A  230  LEU A  235  5                                   6
SHEET    1   A 4 SER A  24  ALA A  27  0
SHEET    2   A 4 ASP A  92  LYS A  97 -1  O  LYS A  97   N  SER A  24
SHEET    3   A 4 GLN A 102  ALA A 106 -1  O  TYR A 105   N  HIS A  93
SHEET    4   A 4 LYS A  78  ALA A  82 -1  N  ALA A  82   O  GLN A 102
SHEET    1   B 4 ILE A  49  ARG A  55  0
SHEET    2   B 4 TYR A  58  ILE A  63 -1  O  ILE A  60   N  SER A  53
SHEET    3   B 4 PHE A  67  HIS A  72 -1  O  SER A  71   N  LEU A  59
SHEET    4   B 4 THR A 113  SER A 118 -1  O  GLU A 115   N  ILE A  70
SHEET    1   C 2 GLN A 253  VAL A 257  0
SHEET    2   C 2 ARG A 260  PHE A 264 -1  O  PHE A 264   N  GLN A 253
LINK        ZN    ZN A5001                 SG  CYS A 268     1555   1555  2.41
LINK        ZN    ZN A5001                 SG  CYS A 248     1555   1555  2.44
LINK        ZN    ZN A5001                 SG  CYS A 265     1555   1555  1.96
LINK        ZN    ZN A5001                 SG  CYS A 245     1555   1555  2.42
LINK         O3'  DT B   6                 P   FOX B   7     1555   1555  1.60
LINK         O3' FOX B   7                 P    DT B   8     1555   1555  1.57
SITE     1 AC1  4 CYS A 245  CYS A 248  CYS A 265  CYS A 268
SITE     1 AC2 10 TYR A  58  HIS A  72  ARG A  74  THR A 113
SITE     2 AC2 10 GLU A 115  TYR A 125  LYS A 129  HOH A5055
SITE     3 AC2 10  DT B   9   DT B  10
CRYST1   92.513   92.513  142.867  90.00  90.00  90.00 P 41 21 2     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      0.010809  0.000000  0.000000        0.00000
SCALE2      0.000000  0.010809  0.000000        0.00000
SCALE3      0.000000  0.000000  0.007000        0.00000
      
PROCHECK
Go to PROCHECK summary
 References