HEADER LYASE 15-OCT-17 6EQU TITLE X-RAY CRYSTAL STRUCTURE OF THE HUMAN CARBONIC ANHYDRASE II ADDUCT WITH TITLE 2 A MEMBRANE-IMPERMEANT INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBONIC ANHYDRASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CARBONATE DEHYDRATASE II,CARBONIC ANHYDRASE C,CAC,CARBONIC COMPND 5 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETM13 KEYWDS HUMAN CARBONIC ANHYDRASE II, MEMBRANE-IMPERMEANT INHIBITOR, COMPLEX, KEYWDS 2 LYASE EXPDTA X-RAY DIFFRACTION AUTHOR V.ALTERIO,G.DE SIMONE,D.ESPOSITO REVDAT 2 17-JAN-24 6EQU 1 REMARK REVDAT 1 13-DEC-17 6EQU 0 JRNL AUTH V.ALTERIO,D.ESPOSITO,S.M.MONTI,C.T.SUPURAN,G.DE SIMONE JRNL TITL CRYSTAL STRUCTURE OF THE HUMAN CARBONIC ANHYDRASE II ADDUCT JRNL TITL 2 WITH 1-(4-SULFAMOYLPHENYL-ETHYL)-2,4,6-TRIPHENYLPYRIDINIUM JRNL TITL 3 PERCHLORATE, A MEMBRANE-IMPERMEANT, ISOFORM SELECTIVE JRNL TITL 4 INHIBITOR. JRNL REF J ENZYME INHIB MED CHEM V. 33 151 2018 JRNL REFN ESSN 1475-6374 JRNL PMID 29199489 JRNL DOI 10.1080/14756366.2017.1405263 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 26849 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM SELECTION REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1306 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.71 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2031 REMARK 3 BIN R VALUE (WORKING SET) : 0.2395 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 122 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2077 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 195 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.70200 REMARK 3 B22 (A**2) : -2.28700 REMARK 3 B33 (A**2) : -0.41400 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.04700 REMARK 3 B23 (A**2) : 0.00000 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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) : 1.226 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.805 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.973 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.908 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 39.09 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 6EQU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1200007032. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 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 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27539 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 25.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.26600 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 5O07 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3 M SODIUM CITRATE, 100 MM TRIS-HCL, REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING 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 20.62950 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 55.96 -141.26 REMARK 500 ALA A 65 -175.27 -171.24 REMARK 500 LYS A 111 -3.01 73.62 REMARK 500 ASN A 244 48.79 -95.28 REMARK 500 LYS A 252 -134.84 51.83 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 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 94 NE2 REMARK 620 2 HIS A 96 NE2 104.9 REMARK 620 3 HIS A 119 ND1 111.4 97.3 REMARK 620 4 BVE A 302 N2 111.8 113.7 116.4 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BVE A 302 DBREF 6EQU A 1 261 UNP P00918 CAH2_HUMAN 1 260 SEQADV 6EQU GLY A 0 UNP P00918 EXPRESSION TAG SEQRES 1 A 261 GLY MET SER HIS HIS TRP GLY TYR GLY LYS HIS ASN GLY SEQRES 2 A 261 PRO GLU HIS TRP HIS LYS ASP PHE PRO ILE ALA LYS GLY SEQRES 3 A 261 GLU ARG GLN SER PRO VAL ASP ILE ASP THR HIS THR ALA SEQRES 4 A 261 LYS TYR ASP PRO SER LEU LYS PRO LEU SER VAL SER TYR SEQRES 5 A 261 ASP GLN ALA THR SER LEU ARG ILE LEU ASN ASN GLY HIS SEQRES 6 A 261 ALA PHE ASN VAL GLU PHE ASP ASP SER GLN ASP LYS ALA SEQRES 7 A 261 VAL LEU LYS GLY GLY PRO LEU ASP GLY THR TYR ARG LEU SEQRES 8 A 261 ILE GLN PHE HIS PHE HIS TRP GLY SER LEU ASP GLY GLN SEQRES 9 A 261 GLY SER GLU HIS THR VAL ASP LYS LYS LYS TYR ALA ALA SEQRES 10 A 261 GLU LEU HIS LEU VAL HIS TRP ASN THR LYS TYR GLY ASP SEQRES 11 A 261 PHE GLY LYS ALA VAL GLN GLN PRO ASP GLY LEU ALA VAL SEQRES 12 A 261 LEU GLY ILE PHE LEU LYS VAL GLY SER ALA LYS PRO GLY SEQRES 13 A 261 LEU GLN LYS VAL VAL ASP VAL LEU ASP SER ILE LYS THR SEQRES 14 A 261 LYS GLY LYS SER ALA ASP PHE THR ASN PHE ASP PRO ARG SEQRES 15 A 261 GLY LEU LEU PRO GLU SER LEU ASP TYR TRP THR TYR PRO SEQRES 16 A 261 GLY SER LEU THR THR PRO PRO LEU LEU GLU CYS VAL THR SEQRES 17 A 261 TRP ILE VAL LEU LYS GLU PRO ILE SER VAL SER SER GLU SEQRES 18 A 261 GLN VAL LEU LYS PHE ARG LYS LEU ASN PHE ASN GLY GLU SEQRES 19 A 261 GLY GLU PRO GLU GLU LEU MET VAL ASP ASN TRP ARG PRO SEQRES 20 A 261 ALA GLN PRO LEU LYS ASN ARG GLN ILE LYS ALA SER PHE SEQRES 21 A 261 LYS HET ZN A 301 1 HET BVE A 302 36 HETNAM ZN ZINC ION HETNAM BVE 4-[2-(2,4,6-TRIPHENYLPYRIDIN-1-IUM-1-YL) HETNAM 2 BVE ETHYL]BENZENESULFONAMIDE FORMUL 2 ZN ZN 2+ FORMUL 3 BVE C31 H27 N2 O2 S 1+ FORMUL 4 HOH *195(H2 O) HELIX 1 AA1 HIS A 15 ASP A 19 5 5 HELIX 2 AA2 PHE A 20 GLY A 25 5 6 HELIX 3 AA3 LYS A 127 GLY A 129 5 3 HELIX 4 AA4 ASP A 130 VAL A 135 1 6 HELIX 5 AA5 LYS A 154 GLY A 156 5 3 HELIX 6 AA6 LEU A 157 LEU A 164 1 8 HELIX 7 AA7 ASP A 165 LYS A 168 5 4 HELIX 8 AA8 ASP A 180 LEU A 185 5 6 HELIX 9 AA9 SER A 219 ARG A 227 1 9 SHEET 1 AA1 2 ASP A 32 ILE A 33 0 SHEET 2 AA1 2 THR A 108 VAL A 109 1 O THR A 108 N ILE A 33 SHEET 1 AA210 LYS A 39 TYR A 40 0 SHEET 2 AA210 LYS A 257 ALA A 258 1 O ALA A 258 N LYS A 39 SHEET 3 AA210 TYR A 191 GLY A 196 -1 N THR A 193 O LYS A 257 SHEET 4 AA210 VAL A 207 LEU A 212 -1 O VAL A 207 N GLY A 196 SHEET 5 AA210 LEU A 141 VAL A 150 1 N GLY A 145 O ILE A 210 SHEET 6 AA210 ALA A 116 ASN A 124 -1 N LEU A 118 O ILE A 146 SHEET 7 AA210 TYR A 88 TRP A 97 -1 N HIS A 94 O HIS A 119 SHEET 8 AA210 PHE A 66 PHE A 70 -1 N VAL A 68 O PHE A 93 SHEET 9 AA210 SER A 56 ASN A 61 -1 N LEU A 57 O GLU A 69 SHEET 10 AA210 SER A 173 ASP A 175 -1 O ALA A 174 N ILE A 59 SHEET 1 AA3 6 LEU A 47 SER A 50 0 SHEET 2 AA3 6 VAL A 78 GLY A 81 -1 O VAL A 78 N SER A 50 SHEET 3 AA3 6 TYR A 88 TRP A 97 -1 O TYR A 88 N LEU A 79 SHEET 4 AA3 6 ALA A 116 ASN A 124 -1 O HIS A 119 N HIS A 94 SHEET 5 AA3 6 LEU A 141 VAL A 150 -1 O ILE A 146 N LEU A 118 SHEET 6 AA3 6 ILE A 216 VAL A 218 1 O ILE A 216 N PHE A 147 LINK NE2 HIS A 94 ZN ZN A 301 1555 1555 2.04 LINK NE2 HIS A 96 ZN ZN A 301 1555 1555 2.03 LINK ND1 HIS A 119 ZN ZN A 301 1555 1555 2.08 LINK ZN ZN A 301 N2 BVE A 302 1555 1555 2.00 CISPEP 1 SER A 29 PRO A 30 0 0.03 CISPEP 2 PRO A 201 PRO A 202 0 0.65 SITE 1 AC1 4 HIS A 94 HIS A 96 HIS A 119 BVE A 302 SITE 1 AC2 13 ASN A 62 HIS A 64 ASN A 67 GLN A 92 SITE 2 AC2 13 HIS A 94 HIS A 96 HIS A 119 PHE A 131 SITE 3 AC2 13 LEU A 198 THR A 199 THR A 200 TRP A 209 SITE 4 AC2 13 ZN A 301 CRYST1 42.141 41.259 71.922 90.00 104.17 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 0.023730 0.000000 0.005991 0.00000 SCALE2 0.000000 0.024237 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014340 0.00000