HEADER OXIDOREDUCTASE 28-JUL-22 7YMB TITLE STRUCTURE OF ALCOHOL DEHYDROGENASE FROM CANDIDA GLABRATA(CGADH) TITLE 2 COMPLEXED WITH NADPH COMPND MOL_ID: 1; COMPND 2 MOLECULE: NADPH-DEPENDENT METHYLGLYOXAL REDUCTASE GRE2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALCOHOL DEHYDROGENASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: [CANDIDA] GLABRATA; SOURCE 3 ORGANISM_COMMON: YEAST, TORULOPSIS GLABRATA; SOURCE 4 ORGANISM_TAXID: 5478; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KETOREDUCATSE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.W.SUN,Y.F.LIU,G.C.XU,Y.NI REVDAT 2 29-MAY-24 7YMB 1 REMARK REVDAT 1 02-AUG-23 7YMB 0 JRNL AUTH Z.W.SUN,Y.NI,G.C.XU JRNL TITL RATIONAL DESIGEN OF CGADH FROM CANDIDA GLABRATA FOR JRNL TITL 2 STEREOCOMPLEMENTARY REDUCTION OF AZACYCLONE. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 30334 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1489 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 24.5900 - 4.0000 0.97 2745 125 0.1596 0.1803 REMARK 3 2 4.0000 - 3.1800 0.96 2636 142 0.1670 0.1935 REMARK 3 3 3.1800 - 2.7800 0.96 2639 149 0.1842 0.2201 REMARK 3 4 2.7700 - 2.5200 0.97 2626 122 0.1893 0.2111 REMARK 3 5 2.5200 - 2.3400 0.97 2678 115 0.1919 0.2592 REMARK 3 6 2.3400 - 2.2000 0.96 2604 130 0.1923 0.2374 REMARK 3 7 2.2000 - 2.0900 0.96 2654 137 0.1965 0.2196 REMARK 3 8 2.0900 - 2.0000 0.96 2590 127 0.2022 0.2390 REMARK 3 9 2.0000 - 1.9200 0.96 2580 162 0.2158 0.2504 REMARK 3 10 1.9200 - 1.8600 0.95 2544 136 0.2347 0.2851 REMARK 3 11 1.8600 - 1.8000 0.94 2549 144 0.2540 0.3242 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.03 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7YMB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031141. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 150 REMARK 200 PH : NULL 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) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MULTILAYER 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 : PROTEUM PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32695 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.739 REMARK 200 RESOLUTION RANGE LOW (A) : 24.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 2.930 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.15600 REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28900 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: NULL REMARK 200 STARTING MODEL: 5B6K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM ACETATE, 0.1M SODIUM REMARK 280 ACETATE PH 4.6, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289.15K 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 24.16100 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: 1250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLU A 345 REMARK 465 ASN A 346 REMARK 465 ALA A 347 REMARK 465 SER A 348 REMARK 465 ALA A 349 REMARK 465 LYS A 350 REMARK 465 LEU A 351 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 THR A 193 OG1 CG2 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 ASN A 69 30.75 70.69 REMARK 500 LEU A 103 -64.26 -121.34 REMARK 500 ALA A 122 36.98 -154.78 REMARK 500 SER A 133 -138.75 -98.54 REMARK 500 GLN A 165 38.07 -87.60 REMARK 500 VAL A 204 -159.59 -78.19 REMARK 500 PHE A 207 -169.26 -111.33 REMARK 500 CYS A 244 -167.42 -173.58 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7YMB A 1 351 UNP A0A0W0CJZ6_CANGB DBREF2 7YMB A A0A0W0CJZ6 1 351 SEQADV 7YMB ASP A 236 UNP A0A0W0CJZ TYR 236 CONFLICT SEQRES 1 A 351 MET THR ALA ALA ASN ASN ASN THR THR VAL PHE VAL SER SEQRES 2 A 351 GLY ALA SER GLY PHE ILE ALA GLN HIS ILE ILE ARG GLN SEQRES 3 A 351 LEU LEU ASP GLN ASN TYR LYS VAL ILE GLY SER VAL ARG SEQRES 4 A 351 SER THR GLU LYS GLY ASP ASN LEU LYS ASN ALA ILE PHE SEQRES 5 A 351 LYS SER ALA ASN PHE ASN TYR GLU ILE VAL LYS ASP ILE SEQRES 6 A 351 ALA ASP LEU ASN ALA PHE ASP PRO VAL PHE GLU LYS HIS SEQRES 7 A 351 GLY LYS ASP ILE LYS VAL VAL LEU HIS THR ALA SER PRO SEQRES 8 A 351 LEU ASN PHE THR THR THR GLU TYR GLU LYS ASP LEU LEU SEQRES 9 A 351 ILE PRO ALA VAL ASN GLY THR LYS GLY ILE LEU GLU SER SEQRES 10 A 351 ILE LYS LYS TYR ALA ALA GLN THR VAL GLU ARG VAL VAL SEQRES 11 A 351 VAL THR SER SER PHE ALA SER HIS THR SER THR VAL ASP SEQRES 12 A 351 MET CYS ASN THR LYS GLY LYS ILE THR GLU ASP SER TRP SEQRES 13 A 351 ASN GLN ASP THR TRP GLU ASN CYS GLN THR ASP ALA VAL SEQRES 14 A 351 ARG ALA TYR PHE GLY SER LYS LYS PHE ALA GLU GLU ALA SEQRES 15 A 351 ALA TRP GLU PHE LEU ASN LYS ASN LYS ASP THR VAL LYS SEQRES 16 A 351 PHE LYS LEU ALA THR VAL ASP PRO VAL TYR VAL PHE GLY SEQRES 17 A 351 PRO GLN ASN HIS ILE GLU PRO GLY LYS LYS VAL LEU ASN SEQRES 18 A 351 VAL SER SER GLU VAL ILE ASN GLN LEU VAL HIS LEU LYS SEQRES 19 A 351 LYS ASP ASP PRO LEU PRO GLN VAL ALA CYS GLY TYR ILE SEQRES 20 A 351 ASP VAL ARG ASP ILE ALA LYS ALA HIS ILE LEU ALA PHE SEQRES 21 A 351 GLN LYS ASP GLU LEU ILE GLY GLN ARG LEU LEU LEU HIS SEQRES 22 A 351 SER GLY LEU PHE THR VAL GLN THR LEU LEU ASP ALA ILE SEQRES 23 A 351 ASN GLU GLN PHE PRO GLU LEU ARG GLY LYS ILE PRO ALA SEQRES 24 A 351 GLY GLU PRO GLY SER ASN LYS PRO GLU ASP LEU LEU THR SEQRES 25 A 351 PRO ILE ASP ASN THR LYS THR LYS LYS LEU LEU GLY PHE SEQRES 26 A 351 GLU PHE ARG ASP LEU LYS THR ILE ILE GLN ASP THR VAL SEQRES 27 A 351 SER GLN ILE LEU GLU ALA GLU ASN ALA SER ALA LYS LEU HET NDP A 401 48 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE FORMUL 2 NDP C21 H30 N7 O17 P3 FORMUL 3 HOH *298(H2 O) HELIX 1 AA1 THR A 2 ASN A 7 1 6 HELIX 2 AA2 GLY A 17 GLN A 30 1 14 HELIX 3 AA3 SER A 40 ILE A 51 1 12 HELIX 4 AA4 PHE A 71 GLY A 79 1 9 HELIX 5 AA5 GLU A 98 LEU A 103 1 6 HELIX 6 AA6 LEU A 103 ALA A 123 1 21 HELIX 7 AA7 SER A 134 HIS A 138 5 5 HELIX 8 AA8 SER A 140 MET A 144 5 5 HELIX 9 AA9 ASP A 167 LYS A 191 1 25 HELIX 10 AB1 ASN A 221 LEU A 233 1 13 HELIX 11 AB2 VAL A 249 LYS A 262 1 14 HELIX 12 AB3 ASP A 263 ILE A 266 5 4 HELIX 13 AB4 VAL A 279 PHE A 290 1 12 HELIX 14 AB5 PRO A 291 ARG A 294 5 4 HELIX 15 AB6 LYS A 306 LEU A 310 5 5 HELIX 16 AB7 ASN A 316 GLY A 324 1 9 HELIX 17 AB8 ASP A 329 ALA A 344 1 16 SHEET 1 AA1 7 PHE A 57 ILE A 61 0 SHEET 2 AA1 7 LYS A 33 VAL A 38 1 N GLY A 36 O ASN A 58 SHEET 3 AA1 7 THR A 9 SER A 13 1 N VAL A 12 O ILE A 35 SHEET 4 AA1 7 ILE A 82 HIS A 87 1 O LEU A 86 N PHE A 11 SHEET 5 AA1 7 ARG A 128 THR A 132 1 O THR A 132 N HIS A 87 SHEET 6 AA1 7 LYS A 197 PRO A 203 1 O LYS A 197 N VAL A 129 SHEET 7 AA1 7 ARG A 269 LEU A 272 1 O LEU A 270 N ASP A 202 SHEET 1 AA2 3 TYR A 205 PHE A 207 0 SHEET 2 AA2 3 ALA A 243 ASP A 248 1 O ILE A 247 N PHE A 207 SHEET 3 AA2 3 GLY A 275 THR A 278 -1 O PHE A 277 N CYS A 244 CRYST1 50.644 48.322 70.475 90.00 96.63 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 0.019746 0.000000 0.002294 0.00000 SCALE2 0.000000 0.020695 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014285 0.00000