HEADER LYASE (OXO-ACID) 03-APR-95 1CNK TITLE X-RAY CRYSTALLOGRAPHIC STUDIES OF ENGINEERED HYDROGEN BOND TITLE 2 NETWORKS IN 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/Q92L; SOURCE 7 EXPRESSION_SYSTEM_GENE: CA2 KEYWDS LYASE (OXO-ACID) EXPDTA X-RAY DIFFRACTION AUTHOR C.A.LESBURG,D.W.CHRISTIANSON REVDAT 3 24-FEB-09 1CNK 1 VERSN REVDAT 2 17-MAY-05 1CNK 1 JRNL REVDAT 1 10-JUL-95 1CNK 0 JRNL AUTH C.A.LESBURG,D.W.CHRISTIANSON JRNL TITL X-RAY CRYSTALLOGRAPHIC STUDIES OF ENGINEERED JRNL TITL 2 HYDROGEN BOND NETWORKS IN A PROTEIN-ZINC BINDING JRNL TITL 3 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 REMARK 1 TITL 2 CARBONIC ANHYDRASE ENHANCES ZINC AFFINITY AND REMARK 1 TITL 3 CATALYTIC EFFICIENCY REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 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 : 12513 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) : 0.176 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 : 6 REMARK 3 SOLVENT ATOMS : 169 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.80 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) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.70 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.50 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 1CNK 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 : 23-JUN-94 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18287 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 (%) : 92.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06700 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) : 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 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 HIS A 4 CB CG ND1 CD2 CE1 NE2 REMARK 480 LYS A 261 CB CG CD CE NZ 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 PRO A 13 -39.16 -35.68 REMARK 500 ALA A 65 -173.43 -171.27 REMARK 500 LYS A 111 -4.57 76.09 REMARK 500 ASN A 244 51.88 -92.94 REMARK 500 LYS A 252 -133.24 52.71 REMARK 500 ASN A 253 31.13 -68.73 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 A 398 DISTANCE = 8.46 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 A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 96 NE2 REMARK 620 2 HIS A 119 ND1 99.4 REMARK 620 3 HIS A 94 NE2 102.2 115.5 REMARK 620 4 HOH A 300 O 91.5 136.1 103.2 REMARK 620 5 SO4 A 262 O2 112.8 119.8 105.8 23.2 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 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 262 DBREF 1CNK A 2 261 UNP P00918 CAH2_HUMAN 1 259 SEQADV 1CNK LEU 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 LEU 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 SO4 A 262 5 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 2 ZN ZN 2+ FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *169(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 96 1555 1555 2.09 LINK ZN ZN A 1 ND1 HIS A 119 1555 1555 1.94 LINK ZN ZN A 1 NE2 HIS A 94 1555 1555 2.06 LINK ZN ZN A 1 O HOH A 300 1555 1555 1.92 LINK ZN ZN A 1 O2 SO4 A 262 1555 1555 1.92 CISPEP 1 SER A 29 PRO A 30 0 -0.05 CISPEP 2 PRO A 201 PRO A 202 0 0.40 SITE 1 ZN 5 HIS A 94 HIS A 96 HIS A 119 HOH A 300 SITE 2 ZN 5 SO4 A 262 SITE 1 AC1 5 HIS A 94 HIS A 96 HIS A 119 SO4 A 262 SITE 2 AC1 5 HOH A 300 SITE 1 AC2 9 ZN A 1 HIS A 94 HIS A 96 HIS A 119 SITE 2 AC2 9 VAL A 121 LEU A 198 THR A 199 TRP A 209 SITE 3 AC2 9 HOH A 300 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 MASTER 276 2 2 7 12 0 7 6 0 0 0 20 END