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PDBsum entry 3ks3

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Lyase PDB id
3ks3
Jmol
Contents
Protein chain
257 a.a.
Ligands
GOL
Metals
_ZN
Waters ×483
HEADER    LYASE                                   20-NOV-09   3KS3
TITLE     HIGH RESOLUTION STRUCTURE OF HUMAN CARBONIC ANHYDRASE II AT
TITLE    2 0.9 A
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: CARBONIC ANHYDRASE 2;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: CARBONIC ANHYDRASE II, CA-II, CARBONATE
COMPND   5 DEHYDRATASE II, CARBONIC ANHYDRASE C, CAC;
COMPND   6 EC: 4.2.1.1;
COMPND   7 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
SOURCE   5 GENE: CA2;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21
KEYWDS    HIGH RESOLUTION, CARBONIC ANHYDRASE, SHORT HYDROGEN BOND
EXPDTA    X-RAY DIFFRACTION
AUTHOR    B.S.AVVARU
REVDAT   1   26-JAN-10 3KS3    0
JRNL        AUTH   B.S.AVVARU,C.U.KIM,K.H.SIPPEL,S.M.GRUNER,
JRNL        AUTH 2 M.AGBANDJE-MCKENNA,D.N.SILVERMAN,R.MCKENNA
JRNL        TITL   A SHORT, STRONG HYDROGEN BOND IN THE ACTIVE SITE OF
JRNL        TITL 2 HUMAN CARBONIC ANHYDRASE II.
JRNL        REF    BIOCHEMISTRY                  V.  49   249 2010
JRNL        REFN                   ISSN 0006-2960
JRNL        PMID   20000378
JRNL        DOI    10.1021/BI902007B
REMARK   1
REMARK   2
REMARK   2 RESOLUTION.    0.90 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : PHENIX (PHENIX.REFINE: 1.5_2)
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN
REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-
REMARK   3               : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO,
REMARK   3               : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL
REMARK   3               : MORIARTY,REETAL PAI,RANDY READ,JANE
REMARK   3               : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM
REMARK   3               : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH,
REMARK   3               : LAURENT STORONI,TOM TERWILLIGER,PETER
REMARK   3               : ZWART
REMARK   3
REMARK   3    REFINEMENT TARGET : ML
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 0.90
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 19.83
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 0.050
REMARK   3   COMPLETENESS FOR RANGE        (%) : 88.4
REMARK   3   NUMBER OF REFLECTIONS             : 158090
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.138
REMARK   3   R VALUE            (WORKING SET) : 0.138
REMARK   3   FREE R VALUE                     : 0.145
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 1.220
REMARK   3   FREE R VALUE TEST SET COUNT      : 1935
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE
REMARK   3     1 19.8377 -  1.9392    0.96    17265   212  0.1521 0.1601
REMARK   3     2  1.9392 -  1.5394    0.96    17013   212  0.1127 0.1159
REMARK   3     3  1.5394 -  1.3448    0.96    16888   203  0.1040 0.1119
REMARK   3     4  1.3448 -  1.2219    0.97    17153   204  0.0959 0.1008
REMARK   3     5  1.2219 -  1.1343    0.94    16651   203  0.0943 0.1058
REMARK   3     6  1.1343 -  1.0675    0.92    16170   210  0.0980 0.1022
REMARK   3     7  1.0675 -  1.0140    0.89    15663   200  0.1137 0.1138
REMARK   3     8  1.0140 -  0.9699    0.83    14619   175  0.1359 0.1442
REMARK   3     9  0.9699 -  0.9325    0.75    13233   166  0.1723 0.1922
REMARK   3    10  0.9325 -  0.9003    0.65    11500   150  0.2244 0.2359
REMARK   3
REMARK   3  BULK SOLVENT MODELLING.
REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL
REMARK   3   SOLVENT RADIUS     : 1.11
REMARK   3   SHRINKAGE RADIUS   : 0.90
REMARK   3   K_SOL              : 0.41
REMARK   3   B_SOL              : 60.48
REMARK   3
REMARK   3  ERROR ESTIMATES.
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.140
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.040
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL
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  TWINNING INFORMATION.
REMARK   3   FRACTION: NULL
REMARK   3   OPERATOR: NULL
REMARK   3
REMARK   3  DEVIATIONS FROM IDEAL VALUES.
REMARK   3                 RMSD          COUNT
REMARK   3   BOND      :  0.009           2216
REMARK   3   ANGLE     :  1.392           3018
REMARK   3   CHIRALITY :  0.099            311
REMARK   3   PLANARITY :  0.008            397
REMARK   3   DIHEDRAL  : 19.152            816
REMARK   3
REMARK   3  TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  : NULL
REMARK   3
REMARK   3  NCS DETAILS
REMARK   3   NUMBER OF NCS GROUPS : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 3KS3 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-DEC-09.
REMARK 100 THE RCSB ID CODE IS RCSB056377.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 14-FEB-09
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : NULL
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : CHESS
REMARK 200  BEAMLINE                       : A1
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9772
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
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   : 164840
REMARK 200  RESOLUTION RANGE HIGH      (A) : 0.900
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 92.3
REMARK 200  DATA REDUNDANCY                : 6.100
REMARK 200  R MERGE                    (I) : 0.07800
REMARK 200  R SYM                      (I) : 0.07800
REMARK 200   FOR THE DATA SET  : 25.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.90
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 0.92
REMARK 200  COMPLETENESS FOR SHELL     (%) : 92.3
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.80
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : 0.58000
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: SHELXS
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 41.27
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,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       20.67950
REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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 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     MET A     1
REMARK 465     SER A     2
REMARK 465     HIS A     3
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  27       55.42   -143.93
REMARK 500    GLU A 106      -61.49    -93.14
REMARK 500    LYS A 111       -3.75     74.09
REMARK 500    PHE A 176       66.50   -152.38
REMARK 500    ASN A 244       47.38    -93.87
REMARK 500    LYS A 252     -139.46     54.18
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 262  ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 402   O
REMARK 620 2 HIS A 119   ND1 118.0
REMARK 620 3 HIS A  94   NE2 110.8 113.6
REMARK 620 4 HIS A  96   NE2 108.2  99.5 105.1
REMARK 620 5 HOH A 707   O    62.6  78.5  87.3 167.0
REMARK 620 N                    1     2     3     4
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 262
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 304
DBREF  3KS3 A    1   261  UNP    P00918   CAH2_HUMAN       1    260
SEQRES   1 A  260  MET SER HIS HIS TRP GLY TYR GLY LYS HIS ASN GLY PRO
SEQRES   2 A  260  GLU HIS TRP HIS LYS ASP PHE PRO ILE ALA LYS GLY GLU
SEQRES   3 A  260  ARG GLN SER PRO VAL ASP ILE ASP THR HIS THR ALA LYS
SEQRES   4 A  260  TYR ASP PRO SER LEU LYS PRO LEU SER VAL SER TYR ASP
SEQRES   5 A  260  GLN ALA THR SER LEU ARG ILE LEU ASN ASN GLY HIS ALA
SEQRES   6 A  260  PHE ASN VAL GLU PHE ASP ASP SER GLN ASP LYS ALA VAL
SEQRES   7 A  260  LEU LYS GLY GLY PRO LEU ASP GLY THR TYR ARG LEU ILE
SEQRES   8 A  260  GLN PHE HIS PHE HIS TRP GLY SER LEU ASP GLY GLN GLY
SEQRES   9 A  260  SER GLU HIS THR VAL ASP LYS LYS LYS TYR ALA ALA GLU
SEQRES  10 A  260  LEU HIS LEU VAL HIS TRP ASN THR LYS TYR GLY ASP PHE
SEQRES  11 A  260  GLY LYS ALA VAL GLN GLN PRO ASP GLY LEU ALA VAL LEU
SEQRES  12 A  260  GLY ILE PHE LEU LYS VAL GLY SER ALA LYS PRO GLY LEU
SEQRES  13 A  260  GLN LYS VAL VAL ASP VAL LEU ASP SER ILE LYS THR LYS
SEQRES  14 A  260  GLY LYS SER ALA ASP PHE THR ASN PHE ASP PRO ARG GLY
SEQRES  15 A  260  LEU LEU PRO GLU SER LEU ASP TYR TRP THR TYR PRO GLY
SEQRES  16 A  260  SER LEU THR THR PRO PRO LEU LEU GLU CYS VAL THR TRP
SEQRES  17 A  260  ILE VAL LEU LYS GLU PRO ILE SER VAL SER SER GLU GLN
SEQRES  18 A  260  VAL LEU LYS PHE ARG LYS LEU ASN PHE ASN GLY GLU GLY
SEQRES  19 A  260  GLU PRO GLU GLU LEU MET VAL ASP ASN TRP ARG PRO ALA
SEQRES  20 A  260  GLN PRO LEU LYS ASN ARG GLN ILE LYS ALA SER PHE LYS
HET     ZN  A 262       1
HET    GOL  A 304       6
HETNAM      ZN ZINC ION
HETNAM     GOL GLYCEROL
FORMUL   2   ZN    ZN 2+
FORMUL   3  GOL    C3 H8 O3
FORMUL   4  HOH   *481(H2 O)
HELIX    1   1 GLY A   12  ASP A   19  5                                   8
HELIX    2   2 PHE A   20  GLY A   25  5                                   6
HELIX    3   3 LYS A  127  GLY A  129  5                                   3
HELIX    4   4 ASP A  130  VAL A  135  1                                   6
HELIX    5   5 LYS A  154  GLY A  156  5                                   3
HELIX    6   6 LEU A  157  LEU A  164  1                                   8
HELIX    7   7 ASP A  165  LYS A  168  5                                   4
HELIX    8   8 ASP A  180  LEU A  185  5                                   6
HELIX    9   9 SER A  219  ARG A  227  1                                   9
SHEET    1   A 2 ASP A  32  ILE A  33  0
SHEET    2   A 2 THR A 108  VAL A 109  1  O  THR A 108   N  ILE A  33
SHEET    1   B10 LYS A  39  TYR A  40  0
SHEET    2   B10 LYS A 257  ALA A 258  1  O  ALA A 258   N  LYS A  39
SHEET    3   B10 TYR A 191  GLY A 196 -1  N  THR A 193   O  LYS A 257
SHEET    4   B10 VAL A 207  LEU A 212 -1  O  VAL A 207   N  GLY A 196
SHEET    5   B10 LEU A 141  VAL A 150  1  N  GLY A 145   O  LEU A 212
SHEET    6   B10 ALA A 116  ASN A 124 -1  N  LEU A 118   O  ILE A 146
SHEET    7   B10 TYR A  88  TRP A  97 -1  N  HIS A  94   O  HIS A 119
SHEET    8   B10 PHE A  66  PHE A  70 -1  N  VAL A  68   O  PHE A  93
SHEET    9   B10 SER A  56  ASN A  61 -1  N  LEU A  57   O  GLU A  69
SHEET   10   B10 SER A 173  ASP A 175 -1  O  ALA A 174   N  ILE A  59
SHEET    1   C 6 LEU A  47  SER A  50  0
SHEET    2   C 6 VAL A  78  GLY A  81 -1  O  LYS A  80   N  SER A  48
SHEET    3   C 6 TYR A  88  TRP A  97 -1  O  TYR A  88   N  LEU A  79
SHEET    4   C 6 ALA A 116  ASN A 124 -1  O  HIS A 119   N  HIS A  94
SHEET    5   C 6 LEU A 141  VAL A 150 -1  O  ILE A 146   N  LEU A 118
SHEET    6   C 6 ILE A 216  VAL A 218  1  O  ILE A 216   N  PHE A 147
LINK        ZN    ZN A 262                 O   HOH A 402     1555   1555  1.90
LINK         ND1 HIS A 119                ZN    ZN A 262     1555   1555  2.02
LINK         NE2 HIS A  94                ZN    ZN A 262     1555   1555  2.03
LINK         NE2 HIS A  96                ZN    ZN A 262     1555   1555  2.04
LINK        ZN    ZN A 262                 O   HOH A 707     1555   1555  2.57
CISPEP   1 SER A   29    PRO A   30          0        -2.73
CISPEP   2 PRO A  201    PRO A  202          0        15.04
SITE     1 AC1  5 HIS A  94  HIS A  96  HIS A 119  HOH A 402
SITE     2 AC1  5 HOH A 707
SITE     1 AC2  8 TYR A   7  ASP A 243  TRP A 245  HOH A 316
SITE     2 AC2  8 HOH A 451  HOH A 608  HOH A 651  HOH A 666
CRYST1   42.354   41.359   72.308  90.00 104.42  90.00 P 1 21 1      2
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      0.023611  0.000000  0.006071        0.00000
SCALE2      0.000000  0.024179  0.000000        0.00000
SCALE3      0.000000  0.000000  0.014280        0.00000
      
PROCHECK
Go to PROCHECK summary
 References