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PDBsum entry 1q39

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Hydrolase PDB id
1q39
Jmol
Contents
Protein chain
257 a.a. *
Metals
_CA ×3
_ZN
Waters ×14
* Residue conservation analysis
HEADER    HYDROLASE                               29-JUL-03   1Q39
TITLE     CRYSTAL STRUCTURE OF THE DNA REPAIR ENZYME ENDONUCLEASE-VIII (NEI)
TITLE    2 FROM E. COLI: THE WT ENZYME AT 2.8 RESOLUTION.
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: ENDONUCLEASE VIII;
COMPND   3 CHAIN: A;
COMPND   4 EC: 3.2.2.-;
COMPND   5 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE   3 ORGANISM_TAXID: 562;
SOURCE   4 GENE: NEI;
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: B834(DE3);
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE   9 EXPRESSION_SYSTEM_PLASMID: PET13A
KEYWDS    HYDROLASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    G.GOLAN,D.O.ZHARKOV,H.FEINBERG,A.S.FERNANDES,E.I.ZAIKA,J.H.KYCIA,
AUTHOR   2 A.P.GROLLMAN,G.SHOHAM
REVDAT   4   13-JUL-11 1Q39    1       VERSN
REVDAT   3   24-FEB-09 1Q39    1       VERSN
REVDAT   2   20-SEP-05 1Q39    1       JRNL
REVDAT   1   03-AUG-04 1Q39    0
JRNL        AUTH   G.GOLAN,D.O.ZHARKOV,H.FEINBERG,A.S.FERNANDES,E.I.ZAIKA,
JRNL        AUTH 2 J.H.KYCIA,A.P.GROLLMAN,G.SHOHAM
JRNL        TITL   STRUCTURE OF THE UNCOMPLEXED DNA REPAIR ENZYME ENDONUCLEASE
JRNL        TITL 2 VIII INDICATES SIGNIFICANT INTERDOMAIN FLEXIBILITY.
JRNL        REF    NUCLEIC ACIDS RES.            V.  33  5006 2005
JRNL        REFN                   ISSN 0305-1048
JRNL        PMID   16145054
JRNL        DOI    10.1093/NAR/GKI796
REMARK   2
REMARK   2 RESOLUTION.    2.80 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : CNS 1.0
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 : NULL
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 29.02
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 81.7
REMARK   3   NUMBER OF REFLECTIONS             : 8158
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) : 0.216
REMARK   3   FREE R VALUE                     : 0.299
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.300
REMARK   3   FREE R VALUE TEST SET COUNT      : 844
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) : 2.80
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.98
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 80.20
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 1181
REMARK   3   BIN R VALUE           (WORKING SET) : 0.3230
REMARK   3   BIN FREE R VALUE                    : 0.4050
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 10.20
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 134
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.035
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 2026
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 4
REMARK   3   SOLVENT ATOMS            : 14
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 32.20
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 54.60
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : NULL
REMARK   3    B22 (A**2) : NULL
REMARK   3    B33 (A**2) : NULL
REMARK   3    B12 (A**2) : NULL
REMARK   3    B13 (A**2) : NULL
REMARK   3    B23 (A**2) : NULL
REMARK   3
REMARK   3  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.34
REMARK   3   ESD FROM SIGMAA              (A) : 0.48
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) : 0.53
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.64
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : 0.007
REMARK   3   BOND ANGLES            (DEGREES) : 1.30
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 23.90
REMARK   3   IMPROPER ANGLES        (DEGREES) : 0.76
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) : 6.170 ; 1.500
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : 9.940 ; 2.000
REMARK   3   SIDE-CHAIN BOND              (A**2) : 7.270 ; 2.000
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : 10.770; 2.500
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED : FLAT MODEL
REMARK   3   KSOL        : 0.32
REMARK   3   BSOL        : 41.01
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  : ION.PARAM
REMARK   3  PARAMETER FILE  4  : NULL
REMARK   3  TOPOLOGY FILE  1   : PROTEIN.TOP
REMARK   3  TOPOLOGY FILE  2   : WATER.TOP
REMARK   3  TOPOLOGY FILE  3   : ION.TOP
REMARK   3  TOPOLOGY FILE  4   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 1Q39 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-AUG-03.
REMARK 100 THE RCSB ID CODE IS RCSB019860.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 12-NOV-01
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 6.5
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : NSLS
REMARK 200  BEAMLINE                       : X25
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.041
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : BRANDEIS - B4
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 10629
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.600
REMARK 200  RESOLUTION RANGE LOW       (A) : 30.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 85.2
REMARK 200  DATA REDUNDANCY                : 2.500
REMARK 200  R MERGE                    (I) : 0.09800
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.64
REMARK 200  COMPLETENESS FOR SHELL     (%) : 88.8
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL
REMARK 200  R MERGE FOR SHELL          (I) : 0.51800
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : NULL
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: THE NEI PROTEIN FROM PDB 1K3X.
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 62.33
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.16M CALCIUM ACETATE, 0.08M SODIUM
REMARK 280  CACODYLATE PH 6.5, 14.4% PEG 8000, VAPOR DIFFUSION, HANGING DROP,
REMARK 280  TEMPERATURE 288K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,-Y,Z
REMARK 290       3555   -X,Y,-Z
REMARK 290       4555   X,-Y,-Z
REMARK 290       5555   X+1/2,Y+1/2,Z+1/2
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+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        0.00000
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        0.00000
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       28.86050
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       39.78900
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000       84.82650
REMARK 290   SMTRY1   6 -1.000000  0.000000  0.000000       28.86050
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       39.78900
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000       84.82650
REMARK 290   SMTRY1   7 -1.000000  0.000000  0.000000       28.86050
REMARK 290   SMTRY2   7  0.000000  1.000000  0.000000       39.78900
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000       84.82650
REMARK 290   SMTRY1   8  1.000000  0.000000  0.000000       28.86050
REMARK 290   SMTRY2   8  0.000000 -1.000000  0.000000       39.78900
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000       84.82650
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: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA,PQS
REMARK 350 TOTAL BURIED SURFACE AREA: 9830 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 44210 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -152.0 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        0.00000
REMARK 350   BIOMT3   2  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   3  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   3  0.000000  0.000000 -1.000000        0.00000
REMARK 350   BIOMT1   4  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   4  0.000000 -1.000000  0.000000        0.00000
REMARK 350   BIOMT3   4  0.000000  0.000000 -1.000000        0.00000
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     PRO A     1
REMARK 465     GLU A     2
REMARK 465     GLY A     3
REMARK 465     PRO A    83
REMARK 465     GLN A    84
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     GLU A   5    CG   CD   OE1  OE2
REMARK 470     ILE A   6    CG1  CG2  CD1
REMARK 470     ARG A   8    CG   CD   NE   CZ   NH1  NH2
REMARK 470     SER A  37    OG
REMARK 470     ASP A  61    CG   OD1  OD2
REMARK 470     GLU A  81    CG   CD   OE1  OE2
REMARK 470     ARG A 124    CG   CD   NE   CZ   NH1  NH2
REMARK 470     GLU A 137    CG   CD   OE1  OE2
REMARK 470     LYS A 140    CG   CD   CE   NZ
REMARK 470     GLU A 235    CG   CD   OE1  OE2
REMARK 470     LEU A 249    CG   CD1  CD2
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    THR A 248   CA  -  C   -  N   ANGL. DEV. = -26.2 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    GLU A   5       15.17   -161.72
REMARK 500    ASP A  61        2.03     83.41
REMARK 500    GLN A  69     -118.04     51.81
REMARK 500    THR A  79       94.82    -54.39
REMARK 500    THR A  86      -36.47     65.10
REMARK 500    SER A 104      -12.94     65.19
REMARK 500    ARG A 149      -23.47    -36.73
REMARK 500    GLN A 214      173.60    -49.79
REMARK 500    HIS A 221      121.48   -170.80
REMARK 500    GLU A 238      -21.01    -38.79
REMARK 500    ARG A 239      -70.83    -86.92
REMARK 500    THR A 248      -79.10    -85.75
REMARK 500    LEU A 249       88.57    -36.58
REMARK 500    SER A 250      149.66   -170.70
REMARK 500    SER A 251      -81.11    -69.58
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500  M RES CSSEQI        ANGLE
REMARK 500    THR A 248         23.43
REMARK 500
REMARK 500 REMARK: NULL
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 A 301  ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 240   SG
REMARK 620 2 CYS A 260   SG  110.2
REMARK 620 3 CYS A 237   SG  123.7 110.5
REMARK 620 4 CYS A 257   SG   93.9 108.8 107.7
REMARK 620 N                    1     2     3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              CA A 302  CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 184   NE2
REMARK 620 2 HIS A 262   O    74.3
REMARK 620 3 HIS A 262   NE2  97.6  57.2
REMARK 620 N                    1     2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              CA A 303  CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 220   NE2
REMARK 620 2 ASP A 195   OD1 142.5
REMARK 620 3 HIS A 199   ND1 137.9  64.4
REMARK 620 4 HIS A 199   NE2 106.7 104.5  41.0
REMARK 620 5 ASP A 195   OD2  93.9  54.4  82.2 112.7
REMARK 620 N                    1     2     3     4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              CA A 304  CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 173   OE1
REMARK 620 2 GLU A 173   O    99.4
REMARK 620 N                    1
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 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 304
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1Q3B   RELATED DB: PDB
REMARK 900 R252A MUTANT AT 2.05 RESOLUTION
REMARK 900 RELATED ID: 1Q3C   RELATED DB: PDB
REMARK 900 E2A MUTANT AT 2.3 RESOLUTION
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 SEQUENCING AND CRYSTALLOGRAPHY CONFIRM THE
REMARK 999 SEQUENCE AS THR A 34 AND ARG A 112.
DBREF  1Q39 A    1   262  UNP    P50465   END8_ECOLI       1    262
SEQADV 1Q39 THR A   34  UNP  P50465    PRO    34 SEE REMARK 999
SEQADV 1Q39 ARG A  112  UNP  P50465    THR   112 SEE REMARK 999
SEQRES   1 A  262  PRO GLU GLY PRO GLU ILE ARG ARG ALA ALA ASP ASN LEU
SEQRES   2 A  262  GLU ALA ALA ILE LYS GLY LYS PRO LEU THR ASP VAL TRP
SEQRES   3 A  262  PHE ALA PHE PRO GLN LEU LYS THR TYR GLN SER GLN LEU
SEQRES   4 A  262  ILE GLY GLN HIS VAL THR HIS VAL GLU THR ARG GLY LYS
SEQRES   5 A  262  ALA LEU LEU THR HIS PHE SER ASN ASP LEU THR LEU TYR
SEQRES   6 A  262  SER HIS ASN GLN LEU TYR GLY VAL TRP ARG VAL VAL ASP
SEQRES   7 A  262  THR GLY GLU GLU PRO GLN THR THR ARG VAL LEU ARG VAL
SEQRES   8 A  262  LYS LEU GLN THR ALA ASP LYS THR ILE LEU LEU TYR SER
SEQRES   9 A  262  ALA SER ASP ILE GLU MET LEU ARG PRO GLU GLN LEU THR
SEQRES  10 A  262  THR HIS PRO PHE LEU GLN ARG VAL GLY PRO ASP VAL LEU
SEQRES  11 A  262  ASP PRO ASN LEU THR PRO GLU VAL VAL LYS GLU ARG LEU
SEQRES  12 A  262  LEU SER PRO ARG PHE ARG ASN ARG GLN PHE ALA GLY LEU
SEQRES  13 A  262  LEU LEU ASP GLN ALA PHE LEU ALA GLY LEU GLY ASN TYR
SEQRES  14 A  262  LEU ARG VAL GLU ILE LEU TRP GLN VAL GLY LEU THR GLY
SEQRES  15 A  262  ASN HIS LYS ALA LYS ASP LEU ASN ALA ALA GLN LEU ASP
SEQRES  16 A  262  ALA LEU ALA HIS ALA LEU LEU GLU ILE PRO ARG PHE SER
SEQRES  17 A  262  TYR ALA THR ARG GLY GLN VAL ASP GLU ASN LYS HIS HIS
SEQRES  18 A  262  GLY ALA LEU PHE ARG PHE LYS VAL PHE HIS ARG ASP GLY
SEQRES  19 A  262  GLU PRO CYS GLU ARG CYS GLY SER ILE ILE GLU LYS THR
SEQRES  20 A  262  THR LEU SER SER ARG PRO PHE TYR TRP CYS PRO GLY CYS
SEQRES  21 A  262  GLN HIS
HET     ZN  A 301       1
HET     CA  A 302       1
HET     CA  A 303       1
HET     CA  A 304       1
HETNAM      ZN ZINC ION
HETNAM      CA CALCIUM ION
FORMUL   2   ZN    ZN 2+
FORMUL   3   CA    3(CA 2+)
FORMUL   6  HOH   *14(H2 O)
HELIX    1   1 ARG A    8  LYS A   18  1                                  11
HELIX    2   2 PHE A   29  THR A   34  5                                   6
HELIX    3   3 TYR A   35  ILE A   40  1                                   6
HELIX    4   4 ARG A  112  LEU A  116  5                                   5
HELIX    5   5 THR A  135  SER A  145  1                                  11
HELIX    6   6 GLN A  152  LEU A  157  1                                   6
HELIX    7   7 GLY A  167  VAL A  178  1                                  12
HELIX    8   8 LYS A  185  LEU A  189  5                                   5
HELIX    9   9 ASN A  190  THR A  211  1                                  22
HELIX   10  10 ASP A  216  HIS A  220  5                                   5
SHEET    1   A 4 ASP A  24  PHE A  27  0
SHEET    2   A 4 LEU A  89  GLN A  94 -1  O  GLN A  94   N  ASP A  24
SHEET    3   A 4 LYS A  98  TYR A 103 -1  O  LEU A 102   N  VAL A  91
SHEET    4   A 4 VAL A  73  ASP A  78 -1  N  VAL A  77   O  THR A  99
SHEET    1   B 4 VAL A  44  ARG A  50  0
SHEET    2   B 4 ALA A  53  PHE A  58 -1  O  LEU A  55   N  GLU A  48
SHEET    3   B 4 THR A  63  HIS A  67 -1  O  LEU A  64   N  THR A  56
SHEET    4   B 4 ASP A 107  LEU A 111 -1  O  LEU A 111   N  THR A  63
SHEET    1   C 2 GLU A 245  LYS A 246  0
SHEET    2   C 2 TYR A 255  TRP A 256 -1  O  TRP A 256   N  GLU A 245
LINK        ZN    ZN A 301                 SG  CYS A 240     1555   1555  2.43
LINK        ZN    ZN A 301                 SG  CYS A 260     1555   1555  2.12
LINK        ZN    ZN A 301                 SG  CYS A 237     1555   1555  2.27
LINK        ZN    ZN A 301                 SG  CYS A 257     1555   1555  2.30
LINK        CA    CA A 302                 NE2 HIS A 184     1555   1555  2.49
LINK        CA    CA A 302                 O   HIS A 262     1555   1555  2.83
LINK        CA    CA A 303                 NE2 HIS A 220     1555   1555  2.10
LINK        CA    CA A 304                 OE1 GLU A 173     1555   1555  3.34
LINK        CA    CA A 304                 O   GLU A 173     1555   1555  2.99
LINK        CA    CA A 302                 NE2 HIS A 262     1555   3555  2.72
LINK        CA    CA A 303                 OD1 ASP A 195     1555   2555  2.32
LINK        CA    CA A 303                 ND1 HIS A 199     1555   2555  3.16
LINK        CA    CA A 303                 NE2 HIS A 199     1555   2555  2.93
LINK        CA    CA A 303                 OD2 ASP A 195     1555   2555  2.44
SITE     1 AC1  4 CYS A 237  CYS A 240  CYS A 257  CYS A 260
SITE     1 AC2  2 HIS A 184  HIS A 262
SITE     1 AC3  3 ASP A 195  HIS A 199  HIS A 220
SITE     1 AC4  3 GLU A 173  TRP A 176  LYS A 228
CRYST1   57.721   79.578  169.653  90.00  90.00  90.00 I 2 2 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      0.017325  0.000000  0.000000        0.00000
SCALE2      0.000000  0.012566  0.000000        0.00000
SCALE3      0.000000  0.000000  0.005894        0.00000
      
PROCHECK
Go to PROCHECK summary
 References