HEADER LYASE (OXO-ACID) 03-APR-95 1CNJ
TITLE X-RAY CRYSTALLOGRAPHIC STUDIES OF ENGINEERED HYDROGEN BOND NETWORKS IN
TITLE 2 A PROTEIN-ZINC BINDING SITE
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
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_PLASMID: PCAM/Q92N;
SOURCE 7 EXPRESSION_SYSTEM_GENE: CA2
KEYWDS LYASE (OXO-ACID)
EXPDTA X-RAY DIFFRACTION
AUTHOR C.A.LESBURG,D.W.CHRISTIANSON
REVDAT 4 07-FEB-24 1CNJ 1 REMARK SEQADV LINK
REVDAT 3 24-FEB-09 1CNJ 1 VERSN
REVDAT 2 17-MAY-05 1CNJ 1 JRNL
REVDAT 1 10-JUL-95 1CNJ 0
JRNL AUTH C.A.LESBURG,D.W.CHRISTIANSON
JRNL TITL X-RAY CRYSTALLOGRAPHIC STUDIES OF ENGINEERED HYDROGEN BOND
JRNL TITL 2 NETWORKS IN A PROTEIN-ZINC BINDING SITE
JRNL REF J.AM.CHEM.SOC. V. 117 6838 1995
JRNL REFN ISSN 0002-7863
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH L.L.KIEFER,S.A.PATERNO,C.A.FIERKE
REMARK 1 TITL HYDROGEN BOND NETWORK IN THE METAL BINDING SITE OF CARBONIC
REMARK 1 TITL 2 ANHYDRASE ENHANCES ZINC AFFINITY AND CATALYTIC EFFICIENCY
REMARK 1 REF TO BE PUBLISHED
REMARK 1 REFN
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
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) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 17556
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING SET) : 0.169
REMARK 3 FREE R VALUE : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
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) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
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 : 2047
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 2
REMARK 3 SOLVENT ATOMS : 203
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.30
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) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
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) : 0.006
REMARK 3 BOND ANGLES (DEGREES) : 1.400
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.40
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.200
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 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1CNJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000172413.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 25-APR-93
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
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) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : AREA DETECTOR
REMARK 200 DETECTOR MANUFACTURER : SIEMENS
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BUDDHA
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18858
REMARK 200 RESOLUTION RANGE HIGH (A) : NULL
REMARK 200 RESOLUTION RANGE LOW (A) : NULL
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 77.0
REMARK 200 DATA REDUNDANCY : 2.800
REMARK 200 R MERGE (I) : 0.10000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: X-PLOR
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 42.97
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16
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 20.85000
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 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 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 ASN A 11 12.08 -148.04
REMARK 500 ALA A 65 -177.06 -176.50
REMARK 500 LYS A 111 -1.64 74.08
REMARK 500 PRO A 202 2.33 -68.64
REMARK 500 ASN A 244 51.11 -93.03
REMARK 500 LYS A 252 -139.25 55.73
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 1 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 94 NE2
REMARK 620 2 HIS A 96 NE2 110.8
REMARK 620 3 HIS A 119 ND1 112.6 103.1
REMARK 620 4 HOH A 418 O 100.4 113.5 116.8
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 HG A 262 HG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 VAL A 135 O
REMARK 620 2 GLN A 137 O 100.5
REMARK 620 3 GLU A 205 O 149.5 92.5
REMARK 620 4 CYS A 206 SG 64.5 86.4 89.2
REMARK 620 5 HOH A 318 O 47.8 142.7 124.8 93.4
REMARK 620 N 1 2 3 4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: ZN
REMARK 800 EVIDENCE_CODE: AUTHOR
REMARK 800 SITE_DESCRIPTION: CATALYTIC CENTER OF CARBONIC ANHYDRASE
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 262
DBREF 1CNJ A 2 261 UNP P00918 CAH2_HUMAN 1 259
SEQADV 1CNJ ASN A 92 UNP P00918 GLN 91 CONFLICT
SEQRES 1 A 259 SER HIS HIS TRP GLY TYR GLY LYS HIS ASN GLY PRO GLU
SEQRES 2 A 259 HIS TRP HIS LYS ASP PHE PRO ILE ALA LYS GLY GLU ARG
SEQRES 3 A 259 GLN SER PRO VAL ASP ILE ASP THR HIS THR ALA LYS TYR
SEQRES 4 A 259 ASP PRO SER LEU LYS PRO LEU SER VAL SER TYR ASP GLN
SEQRES 5 A 259 ALA THR SER LEU ARG ILE LEU ASN ASN GLY HIS ALA PHE
SEQRES 6 A 259 ASN VAL GLU PHE ASP ASP SER GLN ASP LYS ALA VAL LEU
SEQRES 7 A 259 LYS GLY GLY PRO LEU ASP GLY THR TYR ARG LEU ILE ASN
SEQRES 8 A 259 PHE HIS PHE HIS TRP GLY SER LEU ASP GLY GLN GLY SER
SEQRES 9 A 259 GLU HIS THR VAL ASP LYS LYS LYS TYR ALA ALA GLU LEU
SEQRES 10 A 259 HIS LEU VAL HIS TRP ASN THR LYS TYR GLY ASP PHE GLY
SEQRES 11 A 259 LYS ALA VAL GLN GLN PRO ASP GLY LEU ALA VAL LEU GLY
SEQRES 12 A 259 ILE PHE LEU LYS VAL GLY SER ALA LYS PRO GLY LEU GLN
SEQRES 13 A 259 LYS VAL VAL ASP VAL LEU ASP SER ILE LYS THR LYS GLY
SEQRES 14 A 259 LYS SER ALA ASP PHE THR ASN PHE ASP PRO ARG GLY LEU
SEQRES 15 A 259 LEU PRO GLU SER LEU ASP TYR TRP THR TYR PRO GLY SER
SEQRES 16 A 259 LEU THR THR PRO PRO LEU LEU GLU CYS VAL THR TRP ILE
SEQRES 17 A 259 VAL LEU LYS GLU PRO ILE SER VAL SER SER GLU GLN VAL
SEQRES 18 A 259 LEU LYS PHE ARG LYS LEU ASN PHE ASN GLY GLU GLY GLU
SEQRES 19 A 259 PRO GLU GLU LEU MET VAL ASP ASN TRP ARG PRO ALA GLN
SEQRES 20 A 259 PRO LEU LYS ASN ARG GLN ILE LYS ALA SER PHE LYS
HET ZN A 1 1
HET HG A 262 1
HETNAM ZN ZINC ION
HETNAM HG MERCURY (II) ION
FORMUL 2 ZN ZN 2+
FORMUL 3 HG HG 2+
FORMUL 4 HOH *203(H2 O)
HELIX 1 1 TRP A 16 LYS A 18 5 3
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 1 NE2 HIS A 94 1555 1555 2.01
LINK ZN ZN A 1 NE2 HIS A 96 1555 1555 1.98
LINK ZN ZN A 1 ND1 HIS A 119 1555 1555 1.92
LINK ZN ZN A 1 O HOH A 418 1555 1555 2.18
LINK O VAL A 135 HG HG A 262 1555 1555 3.51
LINK O GLN A 137 HG HG A 262 1555 1555 3.07
LINK O GLU A 205 HG HG A 262 1555 1555 3.23
LINK SG CYS A 206 HG HG A 262 1555 1555 2.18
LINK HG HG A 262 O HOH A 318 1555 1555 3.38
CISPEP 1 SER A 29 PRO A 30 0 0.04
CISPEP 2 PRO A 201 PRO A 202 0 0.29
SITE 1 ZN 4 HIS A 94 HIS A 96 HIS A 119 HOH A 418
SITE 1 AC1 5 HIS A 94 HIS A 96 HIS A 119 THR A 199
SITE 2 AC1 5 HOH A 418
SITE 1 AC2 4 VAL A 135 GLN A 137 GLU A 205 CYS A 206
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
(ATOM LINES ARE NOT SHOWN.)
END
