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PDBsum entry 1uga

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Lyase (oxo-acid) PDB id
1uga
Jmol
Contents
Protein chain
258 a.a.
Metals
_ZN
Waters ×121
HEADER    LYASE (OXO-ACID)                        24-JUL-96   1UGA
TITLE     HUMAN CARBONIC ANHYDRASE II[HCAII] (E.C.4.2.1.1) MUTANT
TITLE    2 WITH ALA 65 REPLACED BY PHE (A65F)
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: CARBONIC ANHYDRASE II;
COMPND   3 CHAIN: A;
COMPND   4 EC: 4.2.1.1;
COMPND   5 ENGINEERED: YES;
COMPND   6 MUTATION: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
SOURCE   5 GENE: CAII;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE   9 EXPRESSION_SYSTEM_PLASMID: PCAM;
SOURCE  10 EXPRESSION_SYSTEM_GENE: CAII
KEYWDS    LYASE (OXO-ACID), ACETYLATION, ZINC, POLYMORPHISM, DISEASE
KEYWDS   2 MUTATION
EXPDTA    X-RAY DIFFRACTION
AUTHOR    L.R.SCOLNICK,D.W.CHRISTIANSON
REVDAT   2   24-FEB-09 1UGA    1       VERSN
REVDAT   1   27-JAN-97 1UGA    0
JRNL        AUTH   L.R.SCOLNICK,D.W.CHRISTIANSON
JRNL        TITL   X-RAY CRYSTALLOGRAPHIC STUDIES OF ALANINE-65
JRNL        TITL 2 VARIANTS OF CARBONIC ANHYDRASE II REVEAL THE
JRNL        TITL 3 STRUCTURAL BASIS OF COMPROMISED PROTON TRANSFER IN
JRNL        TITL 4 CATALYSIS.
JRNL        REF    BIOCHEMISTRY                  V.  35 16429 1996
JRNL        REFN                   ISSN 0006-2960
JRNL        PMID   8987974
JRNL        DOI    10.1021/BI9617872
REMARK   1
REMARK   2
REMARK   2 RESOLUTION.    2.00 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : X-PLOR 3.1
REMARK   3   AUTHORS     : BRUNGER
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 6.50
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 2.000
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 88.1
REMARK   3   NUMBER OF REFLECTIONS             : 20445
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : R-FREE
REMARK   3   FREE R VALUE TEST SET SELECTION  : NULL
REMARK   3   R VALUE            (WORKING SET) : 0.154
REMARK   3   FREE R VALUE                     : 0.246
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.000
REMARK   3   FREE R VALUE TEST SET COUNT      : 1021
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : NULL
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.30
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.40
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 9.70
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 1060
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2300
REMARK   3   BIN FREE R VALUE                    : 0.2910
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 10.00
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 120
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 2063
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 1
REMARK   3   SOLVENT ATOMS            : 121
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 23.10
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 20.70
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) : NULL
REMARK   3   ESD FROM SIGMAA              (A) : 0.28
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 12.00
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : 0.009
REMARK   3   BOND ANGLES            (DEGREES) : 1.60
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 25.30
REMARK   3   IMPROPER ANGLES        (DEGREES) : 1.40
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL
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  : PARHCSDX.PRO
REMARK   3  PARAMETER FILE  2  : PARAM-PDB
REMARK   3  PARAMETER FILE  3  : NULL
REMARK   3  TOPOLOGY FILE  1   : TOPHCSDX.PRO
REMARK   3  TOPOLOGY FILE  2   : TOPH-PDB
REMARK   3  TOPOLOGY FILE  3   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 1UGA COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 01-APR-95
REMARK 200  TEMPERATURE           (KELVIN) : 293
REMARK 200  PH                             : 8.0
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : N
REMARK 200  RADIATION SOURCE               : NULL
REMARK 200  BEAMLINE                       : NULL
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU RAXIS IIC
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200  DATA SCALING SOFTWARE          : CCP4 (AGROVATA, ROTAVATA)
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 10085
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.300
REMARK 200  RESOLUTION RANGE LOW       (A) : 6.500
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 88.1
REMARK 200  DATA REDUNDANCY                : 2.000
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : 0.10300
REMARK 200   FOR THE DATA SET  : 6.5300
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.36
REMARK 200  COMPLETENESS FOR SHELL     (%) : 89.7
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.00
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : 0.36900
REMARK 200   FOR SHELL         : 2.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIFFERENCE FOURIER
REMARK 200 SOFTWARE USED: X-PLOR 3.1
REMARK 200 STARTING MODEL: NATIVE CAII, HAKANSSON ET AL. 1992
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 44.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.0
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       20.85000
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 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 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 261    O
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    HIS A  94   CG    HIS A  94   CD2     0.060
REMARK 500    HIS A 119   CG    HIS A 119   CD2     0.062
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    LYS A 111       -6.40     78.31
REMARK 500    ASN A 244       46.77    -89.21
REMARK 500    LYS A 252     -136.35     54.39
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 HIS A  94   NE2
REMARK 620 2 HIS A  96   NE2 107.9
REMARK 620 3 HIS A 119   ND1 102.7 108.1
REMARK 620 4 HOH A 263   O    94.5 115.9 124.5
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 262
DBREF  1UGA A    3   261  UNP    P00918   CAH2_HUMAN       2    259
SEQADV 1UGA PHE A   65  UNP  P00918    ALA    64 ENGINEERED
SEQRES   1 A  258  HIS HIS TRP GLY TYR GLY LYS HIS ASN GLY PRO GLU HIS
SEQRES   2 A  258  TRP HIS LYS ASP PHE PRO ILE ALA LYS GLY GLU ARG GLN
SEQRES   3 A  258  SER PRO VAL ASP ILE ASP THR HIS THR ALA LYS TYR ASP
SEQRES   4 A  258  PRO SER LEU LYS PRO LEU SER VAL SER TYR ASP GLN ALA
SEQRES   5 A  258  THR SER LEU ARG ILE LEU ASN ASN GLY HIS PHE PHE ASN
SEQRES   6 A  258  VAL GLU PHE ASP ASP SER GLN ASP LYS ALA VAL LEU LYS
SEQRES   7 A  258  GLY GLY PRO LEU ASP GLY THR TYR ARG LEU ILE GLN PHE
SEQRES   8 A  258  HIS PHE HIS TRP GLY SER LEU ASP GLY GLN GLY SER GLU
SEQRES   9 A  258  HIS THR VAL ASP LYS LYS LYS TYR ALA ALA GLU LEU HIS
SEQRES  10 A  258  LEU VAL HIS TRP ASN THR LYS TYR GLY ASP PHE GLY LYS
SEQRES  11 A  258  ALA VAL GLN GLN PRO ASP GLY LEU ALA VAL LEU GLY ILE
SEQRES  12 A  258  PHE LEU LYS VAL GLY SER ALA LYS PRO GLY LEU GLN LYS
SEQRES  13 A  258  VAL VAL ASP VAL LEU ASP SER ILE LYS THR LYS GLY LYS
SEQRES  14 A  258  SER ALA ASP PHE THR ASN PHE ASP PRO ARG GLY LEU LEU
SEQRES  15 A  258  PRO GLU SER LEU ASP TYR TRP THR TYR PRO GLY SER LEU
SEQRES  16 A  258  THR THR PRO PRO LEU LEU GLU CYS VAL THR TRP ILE VAL
SEQRES  17 A  258  LEU LYS GLU PRO ILE SER VAL SER SER GLU GLN VAL LEU
SEQRES  18 A  258  LYS PHE ARG LYS LEU ASN PHE ASN GLY GLU GLY GLU PRO
SEQRES  19 A  258  GLU GLU LEU MET VAL ASP ASN TRP ARG PRO ALA GLN PRO
SEQRES  20 A  258  LEU LYS ASN ARG GLN ILE LYS ALA SER PHE LYS
HET     ZN  A 262       1
HETNAM      ZN ZINC ION
FORMUL   2   ZN    ZN 2+
FORMUL   3  HOH   *121(H2 O)
HELIX    1   1 PRO A   13  LYS A   18  5                                   6
HELIX    2   2 PRO A   21  LYS A   24  5                                   4
HELIX    3   3 THR A  125  TYR A  128  5                                   3
HELIX    4   4 PHE A  131  GLN A  136  1                                   6
HELIX    5   5 PRO A  155  ILE A  167  5                                  13
HELIX    6   6 PRO A  181  LEU A  184  5                                   4
HELIX    7   7 SER A  220  LYS A  228  1                                   9
SHEET    1   A 2 LEU A  47  SER A  50  0
SHEET    2   A 2 VAL A  78  GLY A  81 -1  N  LYS A  80   O  SER A  48
SHEET    1   B 3 SER A 173  ASP A 175  0
SHEET    2   B 3 SER A  56  ASN A  61 -1  N  ILE A  59   O  ALA A 174
SHEET    3   B 3 PHE A  66  PHE A  70 -1  N  GLU A  69   O  LEU A  57
SHEET    1   C 5 TYR A 191  GLY A 196  0
SHEET    2   C 5 VAL A 207  LEU A 212 -1  N  VAL A 211   O  TRP A 192
SHEET    3   C 5 LEU A 141  LEU A 148  1  N  LEU A 141   O  THR A 208
SHEET    4   C 5 ALA A 116  ASN A 124 -1  N  HIS A 122   O  ALA A 142
SHEET    5   C 5 TYR A  88  TRP A  97 -1  N  HIS A  96   O  GLU A 117
SHEET    1   D 2 LEU A 148  VAL A 150  0
SHEET    2   D 2 ILE A 216  VAL A 218  1  N  ILE A 216   O  LYS A 149
LINK        ZN    ZN A 262                 NE2 HIS A  94     1555   1555  2.06
LINK        ZN    ZN A 262                 NE2 HIS A  96     1555   1555  2.02
LINK        ZN    ZN A 262                 ND1 HIS A 119     1555   1555  2.05
LINK        ZN    ZN A 262                 O   HOH A 263     1555   1555  2.48
CISPEP   1 SER A   29    PRO A   30          0        -0.13
CISPEP   2 PRO A  201    PRO A  202          0         0.34
SITE     1 AC1  5 HIS A  94  HIS A  96  HIS A 119  THR A 199
SITE     2 AC1  5 HOH A 263
CRYST1   42.700   41.700   73.000  90.00 104.60  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      0.023419  0.000000  0.006100        0.00000
SCALE2      0.000000  0.023981  0.000000        0.00000
SCALE3      0.000000  0.000000  0.014156        0.00000
      
PROCHECK
Go to PROCHECK summary
 References