HEADER METAL BINDING PROTEIN 06-JAN-23 8FR1 TITLE CARBONIC ANHYDRASE IX IN COMPLEX WITH THE ALKYL UREA COMPOUND 3G 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; COMPND 8 MUTATION: 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 INHIBITOR, COMPLEX, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.C.COMBS,R.MCKENNA REVDAT 1 01-FEB-23 8FR1 0 JRNL AUTH J.COMBS,M.BOZDAG,L.D.CRAVEY,A.KOTA,R.MCKENNA,A.ANGELI, JRNL AUTH 2 F.CARTA,C.T.SUPURAN JRNL TITL NEW INSIGHTS INTO CONFORMATIONALLY RESTRICTED CARBONIC JRNL TITL 2 ANHYDRASE INHIBITORS. JRNL REF MOLECULES V. 28 2023 JRNL REFN ESSN 1420-3049 JRNL PMID 36677947 JRNL DOI 10.3390/MOLECULES28020890 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19 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) : 28.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 15937 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 793 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 28.8000 - 3.6326 0.93 2547 141 0.1538 0.1993 REMARK 3 2 3.6326 - 2.8841 0.96 2569 136 0.1778 0.2481 REMARK 3 3 2.8841 - 2.5198 0.94 2514 132 0.2200 0.2484 REMARK 3 4 2.5198 - 2.2895 0.95 2536 136 0.2427 0.3328 REMARK 3 5 2.2895 - 2.1254 0.92 2412 118 0.2643 0.3188 REMARK 3 6 2.1254 - 2.0002 0.96 2566 130 0.2677 0.3402 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.180 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 : 0.007 2132 REMARK 3 ANGLE : 0.913 2896 REMARK 3 CHIRALITY : 0.055 300 REMARK 3 PLANARITY : 0.006 374 REMARK 3 DIHEDRAL : 4.484 1246 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -30.4337 -1.3699 16.1508 REMARK 3 T TENSOR REMARK 3 T11: 0.0405 T22: 0.0394 REMARK 3 T33: 0.0435 T12: 0.0047 REMARK 3 T13: 0.0025 T23: 0.0058 REMARK 3 L TENSOR REMARK 3 L11: 0.6763 L22: 0.7322 REMARK 3 L33: 0.7180 L12: 0.0283 REMARK 3 L13: 0.0032 L23: 0.2101 REMARK 3 S TENSOR REMARK 3 S11: -0.0123 S12: -0.0205 S13: 0.0412 REMARK 3 S21: -0.0434 S22: 0.0262 S23: -0.0442 REMARK 3 S31: -0.0084 S32: -0.0076 S33: 0.0009 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 8FR1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1000271242. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9775 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16029 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 28.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 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) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.33000 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M SODIUM CITRATE, 50 MM TRIS BASE, REMARK 280 PH 7.8, 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 20.80150 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 427 O HOH A 431 2.04 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 50 75.53 -116.32 REMARK 500 LYS A 111 -1.16 72.04 REMARK 500 PHE A 176 65.51 -152.63 REMARK 500 ASN A 244 50.13 -90.60 REMARK 500 LYS A 252 -134.64 53.78 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 106.4 REMARK 620 3 HIS A 119 ND1 119.1 99.7 REMARK 620 4 N84 A 302 NAJ 107.3 103.4 118.7 REMARK 620 5 N84 A 302 SAG 95.5 135.9 102.2 32.6 REMARK 620 N 1 2 3 4 DBREF 8FR1 A 4 261 UNP P00918 CAH2_HUMAN 4 260 SEQADV 8FR1 SER A 65 UNP P00918 ALA 65 ENGINEERED MUTATION SEQADV 8FR1 GLN A 67 UNP P00918 ASN 67 ENGINEERED MUTATION SEQADV 8FR1 THR A 69 UNP P00918 GLU 69 ENGINEERED MUTATION SEQADV 8FR1 LEU A 91 UNP P00918 ILE 91 ENGINEERED MUTATION SEQADV 8FR1 VAL A 131 UNP P00918 PHE 130 ENGINEERED MUTATION SEQADV 8FR1 GLU A 170 UNP P00918 LYS 169 ENGINEERED MUTATION SEQADV 8FR1 ALA A 204 UNP P00918 LEU 203 ENGINEERED MUTATION 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 SER PHE GLN VAL SEQRES 6 A 257 THR 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 LEU 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 VAL 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 GLU 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 ALA 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 N84 A 302 22 HET TRS A 303 8 HETNAM ZN ZINC ION HETNAM N84 4-HYDROXY-3-({[(PYRIDIN-4-YL)METHYL]CARBAMOYL}AMINO) HETNAM 2 N84 BENZENE-1-SULFONAMIDE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 ZN ZN 2+ FORMUL 3 N84 C13 H14 N4 O4 S FORMUL 4 TRS C4 H12 N O3 1+ FORMUL 5 HOH *36(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 LEU A 164 1 11 HELIX 6 AA6 ASP A 165 LYS A 168 5 4 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 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 LEU A 91 O VAL A 121 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 THR 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 VAL A 121 N LEU A 91 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 2.07 LINK NE2 HIS A 96 ZN ZN A 301 1555 1555 2.11 LINK ND1 HIS A 119 ZN ZN A 301 1555 1555 1.98 LINK ZN ZN A 301 NAJ N84 A 302 1555 1555 1.97 LINK ZN ZN A 301 SAG N84 A 302 1555 1555 3.00 CISPEP 1 SER A 29 PRO A 30 0 4.10 CISPEP 2 PRO A 201 PRO A 202 0 9.01 CRYST1 42.503 41.603 72.490 90.00 103.45 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 0.023528 0.000000 0.005627 0.00000 SCALE2 0.000000 0.024037 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014184 0.00000