HEADER LYASE 02-OCT-13 4N0X TITLE ROOM TEMPERATURE CRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II IN TITLE 2 COMPLEX WITH THIOPHENE-2-SULFONAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBONIC ANHYDRASE 2; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: CARBONATE DEHYDRATASE II, CARBONIC ANHYDRASE C, CAC, COMPND 5 CARBONIC ANHYDRASE II, CA-II; 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 KEYWDS MIXED ALPHA/BETA, CARBONATE DEHYDRATASE, CYTOSOLIC, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR S.Z.FISHER,R.F.WILLIAMS REVDAT 2 28-FEB-24 4N0X 1 REMARK REVDAT 1 29-JAN-14 4N0X 0 JRNL AUTH S.Z.FISHER,R.F.WILLIAMS JRNL TITL ROOM TEMPERATURE CRYSTAL STRUCTURE OF HUMAN CARBONIC JRNL TITL 2 ANHYDRASE II IN COMPLEX WITH THIOPHENE-2-SULFONAMIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 28705 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1436 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 26.9209 - 3.5119 0.49 2803 147 0.1412 0.1669 REMARK 3 2 3.5119 - 2.7884 0.49 2857 152 0.1536 0.1655 REMARK 3 3 2.7884 - 2.4362 0.49 2837 148 0.1616 0.1845 REMARK 3 4 2.4362 - 2.2136 0.48 2764 147 0.1431 0.1641 REMARK 3 5 2.2136 - 2.0550 0.48 2788 148 0.1453 0.1686 REMARK 3 6 2.0550 - 1.9339 0.47 2713 146 0.1404 0.1710 REMARK 3 7 1.9339 - 1.8370 0.46 2683 142 0.1403 0.1774 REMARK 3 8 1.8370 - 1.7571 0.46 2629 145 0.1502 0.1888 REMARK 3 9 1.7571 - 1.6895 0.46 2658 135 0.1603 0.2026 REMARK 3 10 1.6895 - 1.6300 0.44 2537 126 0.1536 0.2089 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.070 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 : 0.014 2134 REMARK 3 ANGLE : 1.673 2904 REMARK 3 CHIRALITY : 0.114 304 REMARK 3 PLANARITY : 0.007 377 REMARK 3 DIHEDRAL : 14.034 785 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 4N0X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000082612. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : OSMIC MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28717 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 26.917 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.300 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.6 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M SODIUM CITRATE, 100 MM TRIS, PH REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 20.81450 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: B 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 B 1 REMARK 465 SER B 2 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 HIS B 3 CG ND1 CD2 CE1 NE2 REMARK 470 HIS B 4 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 261 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 HIS B 4 -168.11 -164.26 REMARK 500 ASN B 244 49.02 -95.72 REMARK 500 LYS B 252 -133.16 56.24 REMARK 500 ASN B 253 48.25 -88.08 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 B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 94 NE2 REMARK 620 2 HIS B 96 NE2 105.0 REMARK 620 3 HIS B 119 ND1 113.8 97.8 REMARK 620 4 EVJ B 302 NH 108.3 114.1 117.1 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 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EVJ B 302 DBREF 4N0X B 1 261 UNP P00918 CAH2_HUMAN 1 260 SEQRES 1 B 260 MET SER HIS HIS TRP GLY TYR GLY LYS HIS ASN GLY PRO SEQRES 2 B 260 GLU HIS TRP HIS LYS ASP PHE PRO ILE ALA LYS GLY GLU SEQRES 3 B 260 ARG GLN SER PRO VAL ASP ILE ASP THR HIS THR ALA LYS SEQRES 4 B 260 TYR ASP PRO SER LEU LYS PRO LEU SER VAL SER TYR ASP SEQRES 5 B 260 GLN ALA THR SER LEU ARG ILE LEU ASN ASN GLY HIS ALA SEQRES 6 B 260 PHE ASN VAL GLU PHE ASP ASP SER GLN ASP LYS ALA VAL SEQRES 7 B 260 LEU LYS GLY GLY PRO LEU ASP GLY THR TYR ARG LEU ILE SEQRES 8 B 260 GLN PHE HIS PHE HIS TRP GLY SER LEU ASP GLY GLN GLY SEQRES 9 B 260 SER GLU HIS THR VAL ASP LYS LYS LYS TYR ALA ALA GLU SEQRES 10 B 260 LEU HIS LEU VAL HIS TRP ASN THR LYS TYR GLY ASP PHE SEQRES 11 B 260 GLY LYS ALA VAL GLN GLN PRO ASP GLY LEU ALA VAL LEU SEQRES 12 B 260 GLY ILE PHE LEU LYS VAL GLY SER ALA LYS PRO GLY LEU SEQRES 13 B 260 GLN LYS VAL VAL ASP VAL LEU ASP SER ILE LYS THR LYS SEQRES 14 B 260 GLY LYS SER ALA ASP PHE THR ASN PHE ASP PRO ARG GLY SEQRES 15 B 260 LEU LEU PRO GLU SER LEU ASP TYR TRP THR TYR PRO GLY SEQRES 16 B 260 SER LEU THR THR PRO PRO LEU LEU GLU CYS VAL THR TRP SEQRES 17 B 260 ILE VAL LEU LYS GLU PRO ILE SER VAL SER SER GLU GLN SEQRES 18 B 260 VAL LEU LYS PHE ARG LYS LEU ASN PHE ASN GLY GLU GLY SEQRES 19 B 260 GLU PRO GLU GLU LEU MET VAL ASP ASN TRP ARG PRO ALA SEQRES 20 B 260 GLN PRO LEU LYS ASN ARG GLN ILE LYS ALA SER PHE LYS HET ZN B 301 1 HET EVJ B 302 13 HETNAM ZN ZINC ION HETNAM EVJ THIOPHENE-2-SULFONAMIDE FORMUL 2 ZN ZN 2+ FORMUL 3 EVJ C4 H5 N O2 S2 FORMUL 4 HOH *226(H2 O) HELIX 1 1 GLY B 12 ASP B 19 5 8 HELIX 2 2 PHE B 20 GLY B 25 5 6 HELIX 3 3 LYS B 127 GLY B 129 5 3 HELIX 4 4 ASP B 130 VAL B 135 1 6 HELIX 5 5 LYS B 154 GLY B 156 5 3 HELIX 6 6 LEU B 157 LEU B 164 1 8 HELIX 7 7 ASP B 165 LYS B 168 5 4 HELIX 8 8 ASP B 180 LEU B 185 5 6 HELIX 9 9 SER B 219 ARG B 227 1 9 SHEET 1 A 2 ASP B 32 ILE B 33 0 SHEET 2 A 2 THR B 108 VAL B 109 1 O THR B 108 N ILE B 33 SHEET 1 B10 LYS B 39 TYR B 40 0 SHEET 2 B10 LYS B 257 ALA B 258 1 O ALA B 258 N LYS B 39 SHEET 3 B10 TYR B 191 GLY B 196 -1 N THR B 193 O LYS B 257 SHEET 4 B10 VAL B 207 LEU B 212 -1 O VAL B 207 N GLY B 196 SHEET 5 B10 LEU B 141 VAL B 150 1 N GLY B 145 O ILE B 210 SHEET 6 B10 ALA B 116 ASN B 124 -1 N LEU B 118 O ILE B 146 SHEET 7 B10 TYR B 88 TRP B 97 -1 N HIS B 94 O HIS B 119 SHEET 8 B10 PHE B 66 PHE B 70 -1 N VAL B 68 O PHE B 93 SHEET 9 B10 SER B 56 ASN B 61 -1 N LEU B 57 O GLU B 69 SHEET 10 B10 SER B 173 ASP B 175 -1 O ALA B 174 N ILE B 59 SHEET 1 C 6 LEU B 47 SER B 50 0 SHEET 2 C 6 VAL B 78 GLY B 81 -1 O VAL B 78 N SER B 50 SHEET 3 C 6 TYR B 88 TRP B 97 -1 O TYR B 88 N LEU B 79 SHEET 4 C 6 ALA B 116 ASN B 124 -1 O HIS B 119 N HIS B 94 SHEET 5 C 6 LEU B 141 VAL B 150 -1 O ILE B 146 N LEU B 118 SHEET 6 C 6 ILE B 216 VAL B 218 1 O ILE B 216 N PHE B 147 LINK NE2 HIS B 94 ZN ZN B 301 1555 1555 2.00 LINK NE2 HIS B 96 ZN ZN B 301 1555 1555 2.01 LINK ND1 HIS B 119 ZN ZN B 301 1555 1555 2.06 LINK ZN ZN B 301 NH EVJ B 302 1555 1555 1.92 CISPEP 1 SER B 29 PRO B 30 0 -0.59 CISPEP 2 PRO B 201 PRO B 202 0 10.51 SITE 1 AC1 4 HIS B 94 HIS B 96 HIS B 119 EVJ B 302 SITE 1 AC2 8 HIS B 94 HIS B 96 HIS B 119 LEU B 198 SITE 2 AC2 8 THR B 199 THR B 200 TRP B 209 ZN B 301 CRYST1 42.863 41.629 72.903 90.00 104.53 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 0.023330 0.000000 0.006047 0.00000 SCALE2 0.000000 0.024022 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014170 0.00000