PDB Short entry for 3T82 HEADER LYASE/LYASE INHIBITOR 01-AUG-11 3T82 TITLE HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH ACETYLATED CARBOHYDRATE TITLE 2 SULFAMATES COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBONIC ANHYDRASE 2; COMPND 3 CHAIN: A; 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 ALPHA CARBONIC ANHYDRASE, LYASE-LYASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.HOFMANN,C.K.WANG REVDAT 4 20-MAR-24 3T82 1 HETSYN REVDAT 3 29-JUL-20 3T82 1 REMARK LINK SITE REVDAT 2 10-JUL-13 3T82 1 JRNL REVDAT 1 19-OCT-11 3T82 0 JRNL AUTH M.LOPEZ,H.VU,C.K.WANG,M.G.WOLF,G.GROENHOF,A.INNOCENTI, JRNL AUTH 2 C.T.SUPURAN,S.A.POULSEN JRNL TITL PROMISCUITY OF CARBONIC ANHYDRASE II. UNEXPECTED ESTER JRNL TITL 2 HYDROLYSIS OF CARBOHYDRATE-BASED SULFAMATE INHIBITORS. JRNL REF J.AM.CHEM.SOC. V. 133 18452 2011 JRNL REFN ISSN 0002-7863 JRNL PMID 21958118 JRNL DOI 10.1021/JA207855C REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.4_118) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 31164 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1586 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 24.6693 - 4.4454 0.98 2729 151 0.1531 0.1642 REMARK 3 2 4.4454 - 3.5317 0.98 2722 117 0.1297 0.1500 REMARK 3 3 3.5317 - 3.0863 0.98 2689 163 0.1585 0.1782 REMARK 3 4 3.0863 - 2.8045 0.98 2724 147 0.1614 0.2378 REMARK 3 5 2.8045 - 2.6037 0.98 2692 150 0.1585 0.2210 REMARK 3 6 2.6037 - 2.4504 0.97 2679 147 0.1547 0.2611 REMARK 3 7 2.4504 - 2.3277 0.97 2719 145 0.1519 0.2311 REMARK 3 8 2.3277 - 2.2265 0.96 2641 146 0.1385 0.2041 REMARK 3 9 2.2265 - 2.1408 0.97 2678 134 0.1368 0.1705 REMARK 3 10 2.1408 - 2.0670 0.97 2676 144 0.1331 0.1822 REMARK 3 11 2.0670 - 2.0024 0.94 2629 142 0.1489 0.2283 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 : 0.40 REMARK 3 B_SOL : 38.89 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.360 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) : -0.16160 REMARK 3 B22 (A**2) : -0.58530 REMARK 3 B33 (A**2) : 0.09090 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.23620 REMARK 3 B23 (A**2) : 0.00000 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 : 0.007 2132 REMARK 3 ANGLE : 1.108 2896 REMARK 3 CHIRALITY : 0.074 299 REMARK 3 PLANARITY : 0.005 374 REMARK 3 DIHEDRAL : 20.571 789 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: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 3T82 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000067154. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.953827 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31176 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.9M (NH4)2SO4, 0.1M GLYCINE, PH 9.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 20.70850 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 57.86 -145.41 REMARK 500 ALA A 65 -171.71 -170.70 REMARK 500 LYS A 111 -6.55 73.55 REMARK 500 ASN A 243 51.09 -93.21 REMARK 500 LYS A 251 -137.36 52.50 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 261 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 94 NE2 REMARK 620 2 HIS A 96 NE2 105.9 REMARK 620 3 HIS A 119 ND1 116.1 100.9 REMARK 620 4 SG4 A 300 NAH 114.4 111.1 107.5 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3T83 RELATED DB: PDB REMARK 900 RELATED ID: 3T84 RELATED DB: PDB REMARK 900 RELATED ID: 3T85 RELATED DB: PDB DBREF 3T82 A 1 260 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 261 1 HET SG4 A 300 22 HETNAM ZN ZINC ION HETNAM SG4 3,4-DI-O-ACETYL-6-O-SULFAMOYL-ALPHA-D-GLUCOPYRANOSE HETSYN SG4 3,4-DI-O-ACETYL-6-O-SULFAMOYL-ALPHA-D-GLUCOSE; 3,4-DI- HETSYN 2 SG4 O-ACETYL-6-O-SULFAMOYL-D-GLUCOSE; 3,4-DI-O-ACETYL-6-O- HETSYN 3 SG4 SULFAMOYL-GLUCOSE FORMUL 2 ZN ZN 2+ FORMUL 3 SG4 C10 H17 N O10 S FORMUL 4 HOH *186(H2 O) HELIX 1 1 HIS A 15 ASP A 19 5 5 HELIX 2 2 PHE A 20 GLY A 25 5 6 HELIX 3 3 LYS A 126 GLY A 128 5 3 HELIX 4 4 ASP A 129 VAL A 134 1 6 HELIX 5 5 LYS A 153 GLY A 155 5 3 HELIX 6 6 LEU A 156 LEU A 163 1 8 HELIX 7 7 ASP A 164 LYS A 167 5 4 HELIX 8 8 ASP A 179 LEU A 184 5 6 HELIX 9 9 SER A 218 ARG A 226 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 256 ALA A 257 1 O ALA A 257 N LYS A 39 SHEET 3 B10 TYR A 190 GLY A 195 -1 N THR A 192 O LYS A 256 SHEET 4 B10 VAL A 206 LEU A 211 -1 O VAL A 206 N GLY A 195 SHEET 5 B10 LEU A 140 VAL A 149 1 N GLY A 144 O ILE A 209 SHEET 6 B10 ALA A 116 ASN A 124 -1 N LEU A 118 O ILE A 145 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 PHE A 70 O ILE A 91 SHEET 9 B10 SER A 56 ASN A 61 -1 N ARG A 58 O GLU A 69 SHEET 10 B10 SER A 172 ASP A 174 -1 O ALA A 173 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 140 VAL A 149 -1 O ILE A 145 N LEU A 118 SHEET 6 C 6 ILE A 215 VAL A 217 1 O ILE A 215 N PHE A 146 LINK NE2 HIS A 94 ZN ZN A 261 1555 1555 2.07 LINK NE2 HIS A 96 ZN ZN A 261 1555 1555 2.10 LINK ND1 HIS A 119 ZN ZN A 261 1555 1555 2.11 LINK ZN ZN A 261 NAH SG4 A 300 1555 1555 2.04 CISPEP 1 SER A 29 PRO A 30 0 -0.48 CISPEP 2 PRO A 200 PRO A 201 0 6.40 CRYST1 42.448 41.417 72.208 90.00 104.61 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 0.023558 0.000000 0.006140 0.00000 SCALE2 0.000000 0.024145 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014312 0.00000