HEADER LYASE 15-MAY-23 8JEE TITLE CRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II IN-COMPLEX WITH TITLE 2 LEVOSULPIRIDE AT 2.96 A RESOLUTION 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,CYANAMIDE HYDRATASE CA2; COMPND 6 EC: 4.2.1.1,4.2.1.69; 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 HUMAN CARBONIC ANHYDRASE II, LEVOSULPIRIDE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR S.RASHEED,N.HUDA,S.FALKE,S.Z.FISHER,M.S.AHMAD REVDAT 1 15-MAY-24 8JEE 0 JRNL AUTH S.RASHEED,N.HUDA,M.S.AHMAD JRNL TITL CRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II IN-COMPLEX JRNL TITL 2 WITH LEVOSULPIRIDE AT 2.96 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18_3861: ???) 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) : 2.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 5181 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 254 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 19.9500 - 3.7300 1.00 2503 117 0.1960 0.2304 REMARK 3 2 3.7300 - 2.9600 1.00 2424 137 0.2428 0.2651 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.770 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 : 0.010 2147 REMARK 3 ANGLE : 1.293 2915 REMARK 3 CHIRALITY : 0.074 302 REMARK 3 PLANARITY : 0.007 374 REMARK 3 DIHEDRAL : 15.994 788 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 8JEE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1300037661. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7-8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER D8 QUEST REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5406 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM PLUS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5191 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.960 REMARK 200 RESOLUTION RANGE LOW (A) : 19.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.14 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3KS3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION SOLUTION WAS COMPRISED REMARK 280 OF TRIS-HCL BUFFER (50 MM, PH=7.4), AND 2.9 M AMMONIUM SULFATE. REMARK 280 CRYSTALLIZATION DROP WAS COMPRISED OF HCA-II, ACETOHEXAMIDE AND REMARK 280 RESERVOIR BUFFER., PH 7.4, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 20.88700 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 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 LYS A 24 34.79 -98.31 REMARK 500 TYR A 51 34.13 -84.23 REMARK 500 GLN A 53 38.14 -99.53 REMARK 500 LEU A 57 -51.32 -121.90 REMARK 500 HIS A 64 -41.98 -141.93 REMARK 500 LYS A 111 -7.22 71.11 REMARK 500 LEU A 189 52.02 -110.39 REMARK 500 ASN A 244 52.19 -94.37 REMARK 500 LYS A 252 -133.87 58.52 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 107.4 REMARK 620 3 HIS A 119 ND1 108.5 109.1 REMARK 620 4 U6X A 302 O2 76.6 142.6 104.3 REMARK 620 N 1 2 3 DBREF 8JEE A 4 261 UNP P00918 CAH2_HUMAN 4 260 SEQRES 1 A 257 HIS TRP GLY TYR GLY LYS HIS ASN GLY PRO GLU HIS TRP SEQRES 2 A 257 HIS LYS ASP PHE PRO ILE ALA LYS GLY GLU ARG GLN SER SEQRES 3 A 257 PRO VAL ASP ILE ASP THR HIS THR ALA LYS TYR ASP PRO SEQRES 4 A 257 SER LEU LYS PRO LEU SER VAL SER TYR ASP GLN ALA THR SEQRES 5 A 257 SER LEU ARG ILE LEU ASN ASN GLY HIS ALA PHE ASN VAL SEQRES 6 A 257 GLU PHE ASP ASP SER GLN ASP LYS ALA VAL LEU LYS GLY SEQRES 7 A 257 GLY PRO LEU ASP GLY THR TYR ARG LEU ILE GLN PHE HIS SEQRES 8 A 257 PHE HIS TRP GLY SER LEU ASP GLY GLN GLY SER GLU HIS SEQRES 9 A 257 THR VAL ASP LYS LYS LYS TYR ALA ALA GLU LEU HIS LEU SEQRES 10 A 257 VAL HIS TRP ASN THR LYS TYR GLY ASP PHE GLY LYS ALA SEQRES 11 A 257 VAL GLN GLN PRO ASP GLY LEU ALA VAL LEU GLY ILE PHE SEQRES 12 A 257 LEU LYS VAL GLY SER ALA LYS PRO GLY LEU GLN LYS VAL SEQRES 13 A 257 VAL ASP VAL LEU ASP SER ILE LYS THR LYS GLY LYS SER SEQRES 14 A 257 ALA ASP PHE THR ASN PHE ASP PRO ARG GLY LEU LEU PRO SEQRES 15 A 257 GLU SER LEU ASP TYR TRP THR TYR PRO GLY SER LEU THR SEQRES 16 A 257 THR PRO PRO LEU LEU GLU CYS VAL THR TRP ILE VAL LEU SEQRES 17 A 257 LYS GLU PRO ILE SER VAL SER SER GLU GLN VAL LEU LYS SEQRES 18 A 257 PHE ARG LYS LEU ASN PHE ASN GLY GLU GLY GLU PRO GLU SEQRES 19 A 257 GLU LEU MET VAL ASP ASN TRP ARG PRO ALA GLN PRO LEU SEQRES 20 A 257 LYS ASN ARG GLN ILE LYS ALA SER PHE LYS HET ZN A 301 1 HET U6X A 302 23 HET GOL A 303 6 HET SO4 A 304 5 HET SO4 A 305 5 HETNAM ZN ZINC ION HETNAM U6X LEVOSULPIRIDE HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN U6X ~{N}-[[(2~{S})-1-ETHYLPYRROLIDIN-2-YL]METHYL]-2- HETSYN 2 U6X METHOXY-5-SULFAMOYL-BENZAMIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN ZN 2+ FORMUL 3 U6X C15 H23 N3 O4 S FORMUL 4 GOL C3 H8 O3 FORMUL 5 SO4 2(O4 S 2-) FORMUL 7 HOH *45(H2 O) HELIX 1 AA1 GLY A 12 TRP A 16 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 ASP A 162 1 9 HELIX 6 AA6 VAL A 163 LYS A 168 5 6 HELIX 7 AA7 ASP A 180 LEU A 185 5 6 HELIX 8 AA8 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 LEU A 212 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 ARG A 58 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 LYS A 45 SER A 50 0 SHEET 2 AA3 6 VAL A 78 GLY A 82 -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 VAL A 218 N LYS A 149 LINK NE2 HIS A 94 ZN ZN A 301 1555 1555 2.35 LINK NE2 HIS A 96 ZN ZN A 301 1555 1555 2.14 LINK ND1 HIS A 119 ZN ZN A 301 1555 1555 1.87 LINK ZN ZN A 301 O2 U6X A 302 1555 1555 1.89 CISPEP 1 SER A 29 PRO A 30 0 2.62 CISPEP 2 PRO A 201 PRO A 202 0 2.99 CRYST1 42.323 41.774 71.729 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 0.023628 0.000000 0.005966 0.00000 SCALE2 0.000000 0.023938 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014379 0.00000