HEADER OXIDOREDUCTASE 18-JUL-19 6KIK TITLE CRYSTAL STRUCTURE OF A THERMOSTABLE ALDO-KETO REDUCTASE TM1743 IN TITLE 2 COMPLEX WITH INHIBITOR TOLRESTAT COMPND MOL_ID: 1; COMPND 2 MOLECULE: OXIDOREDUCTASE, ALDO/KETO REDUCTASE FAMILY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA (STRAIN ATCC 43589 / MSB8 / SOURCE 3 DSM 3109 / JCM 10099); SOURCE 4 ORGANISM_TAXID: 243274; SOURCE 5 STRAIN: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099; SOURCE 6 GENE: TM_1743; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A(+) KEYWDS ALDO-KETONE REDUCTASE, TOLRESTAT, COMPETITIVE INHIBITOR, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.Y.ZHANG,X.M.LIU,C.WANG,W.R.TANG REVDAT 3 22-NOV-23 6KIK 1 REMARK REVDAT 2 08-APR-20 6KIK 1 JRNL REVDAT 1 25-SEP-19 6KIK 0 JRNL AUTH C.ZHANG,Z.MIN,X.LIU,C.WANG,Z.WANG,J.SHEN,W.TANG,X.ZHANG, JRNL AUTH 2 D.LIU,X.XU JRNL TITL TOLRESTAT ACTS ATYPICALLY AS A COMPETITIVE INHIBITOR OF THE JRNL TITL 2 THERMOSTABLE ALDO-KETO REDUCTASE TM1743 FROM THERMOTOGA JRNL TITL 3 MARITIMA. JRNL REF FEBS LETT. V. 594 564 2020 JRNL REFN ISSN 0014-5793 JRNL PMID 31573681 JRNL DOI 10.1002/1873-3468.13630 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 51118 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2593 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 39.2560 - 4.2698 1.00 2734 137 0.1661 0.1794 REMARK 3 2 4.2698 - 3.3897 1.00 2606 133 0.1418 0.1539 REMARK 3 3 3.3897 - 2.9614 1.00 2604 138 0.1563 0.2023 REMARK 3 4 2.9614 - 2.6907 1.00 2573 127 0.1701 0.1978 REMARK 3 5 2.6907 - 2.4978 1.00 2561 139 0.1669 0.1992 REMARK 3 6 2.4978 - 2.3506 1.00 2567 125 0.1804 0.1846 REMARK 3 7 2.3506 - 2.2329 1.00 2516 157 0.1698 0.1684 REMARK 3 8 2.2329 - 2.1357 1.00 2569 151 0.1738 0.2069 REMARK 3 9 2.1357 - 2.0535 1.00 2523 134 0.1747 0.1751 REMARK 3 10 2.0535 - 1.9826 1.00 2529 144 0.1746 0.1800 REMARK 3 11 1.9826 - 1.9206 1.00 2524 128 0.1894 0.1949 REMARK 3 12 1.9206 - 1.8657 1.00 2556 128 0.1904 0.2279 REMARK 3 13 1.8657 - 1.8166 1.00 2528 147 0.1972 0.1970 REMARK 3 14 1.8166 - 1.7723 1.00 2515 131 0.2016 0.1995 REMARK 3 15 1.7723 - 1.7320 1.00 2511 149 0.1902 0.2365 REMARK 3 16 1.7320 - 1.6951 1.00 2509 143 0.1955 0.2305 REMARK 3 17 1.6951 - 1.6612 1.00 2536 133 0.2041 0.2126 REMARK 3 18 1.6612 - 1.6299 1.00 2528 115 0.2087 0.2123 REMARK 3 19 1.6299 - 1.6010 1.00 2536 134 0.2130 0.2504 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.37 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 : 0.005 2277 REMARK 3 ANGLE : 0.834 3079 REMARK 3 CHIRALITY : 0.052 342 REMARK 3 PLANARITY : 0.005 394 REMARK 3 DIHEDRAL : 3.222 1383 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 6KIK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300013069. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97861 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 : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51163 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.601 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.60 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45000 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: PHASER REMARK 200 STARTING MODEL: 5DAN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 100000, 0.1 M SODIUM ACETATE REMARK 280 TRIHYDRATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.99667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 61.99333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 61.99333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.99667 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: 560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12370 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 PHE A 26 -85.01 -104.86 REMARK 500 ALA A 245 -72.13 -55.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TOL A 301 DBREF 6KIK A 1 274 UNP Q9X265 Q9X265_THEMA 1 274 SEQADV 6KIK SER A 0 UNP Q9X265 EXPRESSION TAG SEQRES 1 A 275 SER MET LEU TYR LYS GLU LEU GLY ARG THR GLY GLU GLU SEQRES 2 A 275 ILE PRO ALA LEU GLY LEU GLY THR TRP GLY ILE GLY GLY SEQRES 3 A 275 PHE GLU THR PRO ASP TYR SER ARG ASP GLU GLU MET VAL SEQRES 4 A 275 GLU LEU LEU LYS THR ALA ILE LYS MET GLY TYR THR HIS SEQRES 5 A 275 ILE ASP THR ALA GLU TYR TYR GLY GLY GLY HIS THR GLU SEQRES 6 A 275 GLU LEU ILE GLY LYS ALA ILE LYS ASP PHE ARG ARG GLU SEQRES 7 A 275 ASP LEU PHE ILE VAL SER LYS VAL TRP PRO THR HIS LEU SEQRES 8 A 275 ARG ARG ASP ASP LEU LEU ARG SER LEU GLU ASN THR LEU SEQRES 9 A 275 LYS ARG LEU ASP THR ASP TYR VAL ASP LEU TYR LEU ILE SEQRES 10 A 275 HIS TRP PRO ASN PRO GLU ILE PRO LEU GLU GLU THR LEU SEQRES 11 A 275 SER ALA MET ALA GLU GLY VAL ARG GLN GLY LEU ILE ARG SEQRES 12 A 275 TYR ILE GLY VAL SER ASN PHE ASP ARG ARG LEU LEU GLU SEQRES 13 A 275 GLU ALA ILE SER LYS SER GLN GLU PRO ILE VAL CYS ASP SEQRES 14 A 275 GLN VAL LYS TYR ASN ILE GLU ASP ARG ASP PRO GLU ARG SEQRES 15 A 275 ASP GLY LEU LEU GLU PHE CYS GLN LYS ASN GLY VAL THR SEQRES 16 A 275 LEU VAL ALA TYR SER PRO LEU ARG ARG THR LEU LEU SER SEQRES 17 A 275 GLU LYS THR LYS ARG THR LEU GLU GLU ILE ALA LYS ASN SEQRES 18 A 275 HIS GLY ALA THR ILE TYR GLN ILE MET LEU ALA TRP LEU SEQRES 19 A 275 LEU ALA LYS PRO ASN VAL VAL ALA ILE PRO LYS ALA GLY SEQRES 20 A 275 ARG VAL GLU HIS LEU ARG GLU ASN LEU LYS ALA THR GLU SEQRES 21 A 275 ILE LYS LEU SER GLU GLU GLU MET LYS LEU LEU ASP SER SEQRES 22 A 275 LEU GLY HET TOL A 301 24 HETNAM TOL TOLRESTAT FORMUL 2 TOL C16 H14 F3 N O3 S FORMUL 3 HOH *331(H2 O) HELIX 1 AA1 ARG A 33 GLY A 48 1 16 HELIX 2 AA2 TYR A 57 GLY A 60 5 4 HELIX 3 AA3 GLY A 61 ILE A 71 1 11 HELIX 4 AA4 LYS A 72 PHE A 74 5 3 HELIX 5 AA5 ARG A 75 LEU A 79 5 5 HELIX 6 AA6 TRP A 86 LEU A 90 5 5 HELIX 7 AA7 ARG A 91 ASP A 107 1 17 HELIX 8 AA8 PRO A 124 GLN A 138 1 15 HELIX 9 AA9 ASP A 150 SER A 161 1 12 HELIX 10 AB1 ARG A 177 ASP A 182 1 6 HELIX 11 AB2 GLY A 183 ASN A 191 1 9 HELIX 12 AB3 SER A 207 GLY A 222 1 16 HELIX 13 AB4 THR A 224 ALA A 235 1 12 HELIX 14 AB5 ARG A 247 ALA A 257 1 11 HELIX 15 AB6 THR A 258 ILE A 260 5 3 HELIX 16 AB7 SER A 263 SER A 272 1 10 SHEET 1 AA1 2 TYR A 3 GLU A 5 0 SHEET 2 AA1 2 GLU A 12 PRO A 14 -1 O ILE A 13 N LYS A 4 SHEET 1 AA2 8 LEU A 18 GLY A 19 0 SHEET 2 AA2 8 HIS A 51 ASP A 53 1 O HIS A 51 N LEU A 18 SHEET 3 AA2 8 PHE A 80 VAL A 85 1 O VAL A 82 N ILE A 52 SHEET 4 AA2 8 VAL A 111 ILE A 116 1 O LEU A 115 N VAL A 85 SHEET 5 AA2 8 ILE A 141 SER A 147 1 O TYR A 143 N ASP A 112 SHEET 6 AA2 8 ILE A 165 LYS A 171 1 O VAL A 166 N ILE A 144 SHEET 7 AA2 8 THR A 194 TYR A 198 1 O THR A 194 N VAL A 166 SHEET 8 AA2 8 VAL A 239 ILE A 242 1 O VAL A 240 N ALA A 197 SITE 1 AC1 11 TRP A 21 GLU A 27 TYR A 57 TYR A 58 SITE 2 AC1 11 LYS A 84 TRP A 86 PRO A 87 HIS A 117 SITE 3 AC1 11 TRP A 118 HOH A 447 HOH A 592 CRYST1 84.594 84.594 92.990 90.00 90.00 120.00 P 31 2 1 6 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 0.011821 0.006825 0.000000 0.00000 SCALE2 0.000000 0.013650 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010754 0.00000