HEADER PROTON TRANSPORT 16-MAY-19 6RQW TITLE X-RAY CRYSTAL STRUCTURE OF PERDEUTERATED (D) SMALL MONOCLINIC UNIT TITLE 2 CELL CA IX SV. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBONIC ANHYDRASE 9; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CARBONATE DEHYDRATASE IX,CARBONIC ANHYDRASE IX,CAIX,MEMBRANE COMPND 5 ANTIGEN MN,P54/58N,RENAL CELL CARCINOMA-ASSOCIATED ANTIGEN G250,RCC- COMPND 6 ASSOCIATED ANTIGEN G250,PMW1; COMPND 7 EC: 4.2.1.1; COMPND 8 ENGINEERED: YES; COMPND 9 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: CA9, G250, MN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CARBONIC ANHYDRASE, CA IX, SURFACE VARIANT, PROTON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR Z.FISHER,K.KORUZA REVDAT 3 24-JAN-24 6RQW 1 REMARK REVDAT 2 16-OCT-19 6RQW 1 JRNL REVDAT 1 11-SEP-19 6RQW 0 JRNL AUTH K.KORUZA,B.LAFUMAT,M.NYBLOM,B.P.MAHON,W.KNECHT,R.MCKENNA, JRNL AUTH 2 S.Z.FISHER JRNL TITL STRUCTURAL COMPARISON OF PROTIATED, H/D-EXCHANGED AND JRNL TITL 2 DEUTERATED HUMAN CARBONIC ANHYDRASE IX. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 75 895 2019 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 31588921 JRNL DOI 10.1107/S2059798319010027 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 39435 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 1869 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 40.3412 - 3.4988 0.99 2925 155 0.1437 0.1870 REMARK 3 2 3.4988 - 2.7773 1.00 2914 142 0.1697 0.1752 REMARK 3 3 2.7773 - 2.4263 1.00 2899 143 0.1794 0.2102 REMARK 3 4 2.4263 - 2.2045 1.00 2939 106 0.1764 0.2102 REMARK 3 5 2.2045 - 2.0465 1.00 2879 147 0.1718 0.2131 REMARK 3 6 2.0465 - 1.9258 1.00 2920 133 0.1698 0.1832 REMARK 3 7 1.9258 - 1.8294 1.00 2891 132 0.1816 0.2381 REMARK 3 8 1.8294 - 1.7497 1.00 2876 157 0.1853 0.2186 REMARK 3 9 1.7497 - 1.6824 1.00 2886 147 0.1858 0.2274 REMARK 3 10 1.6824 - 1.6243 1.00 2858 155 0.2183 0.2751 REMARK 3 11 1.6243 - 1.5735 1.00 2856 138 0.2616 0.2949 REMARK 3 12 1.5735 - 1.5286 1.00 2856 159 0.3006 0.3075 REMARK 3 13 1.5286 - 1.4883 1.00 2867 155 0.3579 0.3686 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.23 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 : 0.015 2154 REMARK 3 ANGLE : 1.344 2954 REMARK 3 CHIRALITY : 0.100 322 REMARK 3 PLANARITY : 0.011 392 REMARK 3 DIHEDRAL : 25.156 824 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 6RQW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1292102426. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX IV REMARK 200 BEAMLINE : BIOMAX REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39461 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.488 REMARK 200 RESOLUTION RANGE LOW (A) : 40.326 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.78100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5DVX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) PEG 4000, 0.2 M AMMONIUM REMARK 280 FORMATE, 0.1 M TRIS-HCL PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K 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 32.54500 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 ASP A 146 -176.12 61.41 REMARK 500 PRO A 148 158.17 -46.17 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 226 NE2 REMARK 620 2 HIS A 228 NE2 102.3 REMARK 620 3 HIS A 251 ND1 113.6 97.5 REMARK 620 4 FMT A 402 O2 89.6 164.4 86.8 REMARK 620 5 HOH A 508 O 103.9 98.3 134.8 68.7 REMARK 620 N 1 2 3 4 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 402 DBREF 6RQW A 140 395 UNP Q16790 CAH9_HUMAN 140 395 SEQADV 6RQW SER A 174 UNP Q16790 CYS 174 ENGINEERED MUTATION SEQADV 6RQW SER A 183 UNP Q16790 LEU 183 ENGINEERED MUTATION SEQADV 6RQW LYS A 213 UNP Q16790 ALA 213 ENGINEERED MUTATION SEQADV 6RQW LYS A 258 UNP Q16790 ALA 258 ENGINEERED MUTATION SEQADV 6RQW TYR A 259 UNP Q16790 PHE 259 ENGINEERED MUTATION SEQADV 6RQW SER A 350 UNP Q16790 MET 350 ENGINEERED MUTATION SEQRES 1 A 256 HIS TRP ARG TYR GLY GLY ASP PRO PRO TRP PRO ARG VAL SEQRES 2 A 256 SER PRO ALA CYS ALA GLY ARG PHE GLN SER PRO VAL ASP SEQRES 3 A 256 ILE ARG PRO GLN LEU ALA ALA PHE SER PRO ALA LEU ARG SEQRES 4 A 256 PRO LEU GLU LEU SER GLY PHE GLN LEU PRO PRO LEU PRO SEQRES 5 A 256 GLU LEU ARG LEU ARG ASN ASN GLY HIS SER VAL GLN LEU SEQRES 6 A 256 THR LEU PRO PRO GLY LEU GLU MET LYS LEU GLY PRO GLY SEQRES 7 A 256 ARG GLU TYR ARG ALA LEU GLN LEU HIS LEU HIS TRP GLY SEQRES 8 A 256 ALA ALA GLY ARG PRO GLY SER GLU HIS THR VAL GLU GLY SEQRES 9 A 256 HIS ARG PHE PRO ALA GLU ILE HIS VAL VAL HIS LEU SER SEQRES 10 A 256 THR LYS TYR ALA ARG VAL ASP GLU ALA LEU GLY ARG PRO SEQRES 11 A 256 GLY GLY LEU ALA VAL LEU ALA ALA PHE LEU GLU GLU GLY SEQRES 12 A 256 PRO GLU GLU ASN SER ALA TYR GLU GLN LEU LEU SER ARG SEQRES 13 A 256 LEU GLU GLU ILE ALA GLU GLU GLY SER GLU THR GLN VAL SEQRES 14 A 256 PRO GLY LEU ASP ILE SER ALA LEU LEU PRO SER ASP PHE SEQRES 15 A 256 SER ARG TYR PHE GLN TYR GLU GLY SER LEU THR THR PRO SEQRES 16 A 256 PRO CYS ALA GLN GLY VAL ILE TRP THR VAL PHE ASN GLN SEQRES 17 A 256 THR VAL SER LEU SER ALA LYS GLN LEU HIS THR LEU SER SEQRES 18 A 256 ASP THR LEU TRP GLY PRO GLY ASP SER ARG LEU GLN LEU SEQRES 19 A 256 ASN PHE ARG ALA THR GLN PRO LEU ASN GLY ARG VAL ILE SEQRES 20 A 256 GLU ALA SER PHE PRO ALA GLY VAL ASP HET ZN A 401 1 HET FMT A 402 3 HETNAM ZN ZINC ION HETNAM FMT FORMIC ACID FORMUL 2 ZN ZN 2+ FORMUL 3 FMT C H2 O2 FORMUL 4 HOH *209(H2 O) HELIX 1 AA1 PRO A 148 VAL A 152 5 5 HELIX 2 AA2 SER A 153 GLY A 158 5 6 HELIX 3 AA3 ARG A 167 ALA A 171 5 5 HELIX 4 AA4 ARG A 261 LEU A 266 1 6 HELIX 5 AA5 ASN A 286 SER A 294 1 9 HELIX 6 AA6 ARG A 295 ALA A 300 5 6 HELIX 7 AA7 ASP A 312 LEU A 317 5 6 HELIX 8 AA8 SER A 352 THR A 362 1 11 SHEET 1 AA1 2 ASP A 165 ILE A 166 0 SHEET 2 AA1 2 THR A 240 VAL A 241 1 O THR A 240 N ILE A 166 SHEET 1 AA210 ALA A 172 PHE A 173 0 SHEET 2 AA210 GLU A 387 ALA A 388 1 O ALA A 388 N ALA A 172 SHEET 3 AA210 TYR A 324 SER A 330 -1 N GLN A 326 O GLU A 387 SHEET 4 AA210 GLN A 338 PHE A 345 -1 O VAL A 340 N GLY A 329 SHEET 5 AA210 LEU A 272 GLU A 281 1 N ALA A 276 O THR A 343 SHEET 6 AA210 ALA A 248 SER A 256 -1 N VAL A 252 O LEU A 275 SHEET 7 AA210 ARG A 218 TRP A 229 -1 N LEU A 223 O VAL A 253 SHEET 8 AA210 VAL A 202 THR A 205 -1 N LEU A 204 O LEU A 225 SHEET 9 AA210 LEU A 193 ASN A 197 -1 N ARG A 194 O THR A 205 SHEET 10 AA210 GLU A 305 VAL A 308 -1 O VAL A 308 N LEU A 193 SHEET 1 AA3 6 GLU A 181 SER A 183 0 SHEET 2 AA3 6 GLU A 211 GLY A 215 -1 O GLU A 211 N SER A 183 SHEET 3 AA3 6 ARG A 218 TRP A 229 -1 O ARG A 218 N LEU A 214 SHEET 4 AA3 6 ALA A 248 SER A 256 -1 O VAL A 253 N LEU A 223 SHEET 5 AA3 6 LEU A 272 GLU A 281 -1 O LEU A 275 N VAL A 252 SHEET 6 AA3 6 VAL A 349 LEU A 351 1 O VAL A 349 N GLU A 280 SSBOND 1 CYS A 156 CYS A 336 1555 1555 2.09 LINK NE2 HIS A 226 ZN ZN A 401 1555 1555 2.06 LINK NE2 HIS A 228 ZN ZN A 401 1555 1555 2.08 LINK ND1 HIS A 251 ZN ZN A 401 1555 1555 2.08 LINK ZN ZN A 401 O2 FMT A 402 1555 1555 2.33 LINK ZN ZN A 401 O HOH A 508 1555 1555 2.01 CISPEP 1 SER A 162 PRO A 163 0 -0.66 CISPEP 2 LEU A 190 PRO A 191 0 2.56 CISPEP 3 PRO A 334 PRO A 335 0 11.29 SITE 1 AC1 5 HIS A 226 HIS A 228 HIS A 251 FMT A 402 SITE 2 AC1 5 HOH A 508 SITE 1 AC2 7 HIS A 226 HIS A 251 LEU A 331 THR A 332 SITE 2 AC2 7 ZN A 401 HOH A 508 HOH A 553 CRYST1 44.390 65.090 46.600 90.00 114.71 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 0.022528 0.000000 0.010365 0.00000 SCALE2 0.000000 0.015363 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023622 0.00000