PDB Short entry for 4GA8 HEADER OXIDOREDUCTASE 25-JUL-12 4GA8 TITLE HUMAN AKR1B10 MUTANT V301L COMPLEXED WITH NADP+ AND SORBINIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALDO-KETO REDUCTASE FAMILY 1 MEMBER B10; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ARL-1, ALDOSE REDUCTASE-LIKE, ALDOSE REDUCTASE-RELATED COMPND 5 PROTEIN, ARP, HARP, SMALL INTESTINE REDUCTASE, SI REDUCTASE; COMPND 6 EC: 1.1.1.-; 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: AKR1B10, AKR1B11; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30-XA/LIC KEYWDS TIM BARREL, ALDO-KETO REDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.COUSIDO-SIAH,F.X.RUIZ FIGUERAS,A.MITSCHLER,A.PODJARNY REVDAT 3 13-SEP-23 4GA8 1 REMARK SEQADV REVDAT 2 15-NOV-17 4GA8 1 REMARK REVDAT 1 07-AUG-13 4GA8 0 REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 26139 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1329 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 24.4833 - 4.0341 1.00 2814 158 0.1236 0.1603 REMARK 3 2 4.0341 - 3.2043 1.00 2755 152 0.1341 0.2071 REMARK 3 3 3.2043 - 2.7999 1.00 2760 150 0.1611 0.2293 REMARK 3 4 2.7999 - 2.5442 1.00 2758 154 0.1703 0.2034 REMARK 3 5 2.5442 - 2.3620 1.00 2764 146 0.1659 0.2122 REMARK 3 6 2.3620 - 2.2228 1.00 2752 137 0.1680 0.2282 REMARK 3 7 2.2228 - 2.1116 1.00 2742 151 0.1702 0.2318 REMARK 3 8 2.1116 - 2.0197 1.00 2741 151 0.1773 0.2884 REMARK 3 9 2.0197 - 1.9420 0.99 2724 130 0.2023 0.2628 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.99 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 2871 REMARK 3 ANGLE : 1.276 3929 REMARK 3 CHIRALITY : 0.079 420 REMARK 3 PLANARITY : 0.006 507 REMARK 3 DIHEDRAL : 12.932 1094 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 4GA8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000073933. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : DOUBLE MIRRORS MONOCHROMATOR REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26168 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.942 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : 0.07500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1ZUA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 6000, 100 MM SODIUM REMARK 280 CACODYLATE, PH 9.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 26.05167 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 52.10333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.07750 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 65.12917 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 13.02583 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 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 10 -1.05 74.10 REMARK 500 ASP A 127 26.05 -73.76 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 NAP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SBI A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZUA RELATED DB: PDB DBREF 4GA8 A 1 316 UNP O60218 AK1BA_HUMAN 1 316 SEQADV 4GA8 LEU A 301 UNP O60218 VAL 301 ENGINEERED MUTATION SEQRES 1 A 316 MET ALA THR PHE VAL GLU LEU SER THR LYS ALA LYS MET SEQRES 2 A 316 PRO ILE VAL GLY LEU GLY THR TRP LYS SER PRO LEU GLY SEQRES 3 A 316 LYS VAL LYS GLU ALA VAL LYS VAL ALA ILE ASP ALA GLY SEQRES 4 A 316 TYR ARG HIS ILE ASP CYS ALA TYR VAL TYR GLN ASN GLU SEQRES 5 A 316 HIS GLU VAL GLY GLU ALA ILE GLN GLU LYS ILE GLN GLU SEQRES 6 A 316 LYS ALA VAL LYS ARG GLU ASP LEU PHE ILE VAL SER LYS SEQRES 7 A 316 LEU TRP PRO THR PHE PHE GLU ARG PRO LEU VAL ARG LYS SEQRES 8 A 316 ALA PHE GLU LYS THR LEU LYS ASP LEU LYS LEU SER TYR SEQRES 9 A 316 LEU ASP VAL TYR LEU ILE HIS TRP PRO GLN GLY PHE LYS SEQRES 10 A 316 SER GLY ASP ASP LEU PHE PRO LYS ASP ASP LYS GLY ASN SEQRES 11 A 316 ALA ILE GLY GLY LYS ALA THR PHE LEU ASP ALA TRP GLU SEQRES 12 A 316 ALA MET GLU GLU LEU VAL ASP GLU GLY LEU VAL LYS ALA SEQRES 13 A 316 LEU GLY VAL SER ASN PHE SER HIS PHE GLN ILE GLU LYS SEQRES 14 A 316 LEU LEU ASN LYS PRO GLY LEU LYS TYR LYS PRO VAL THR SEQRES 15 A 316 ASN GLN VAL GLU CYS HIS PRO TYR LEU THR GLN GLU LYS SEQRES 16 A 316 LEU ILE GLN TYR CYS HIS SER LYS GLY ILE THR VAL THR SEQRES 17 A 316 ALA TYR SER PRO LEU GLY SER PRO ASP ARG PRO TRP ALA SEQRES 18 A 316 LYS PRO GLU ASP PRO SER LEU LEU GLU ASP PRO LYS ILE SEQRES 19 A 316 LYS GLU ILE ALA ALA LYS HIS LYS LYS THR ALA ALA GLN SEQRES 20 A 316 VAL LEU ILE ARG PHE HIS ILE GLN ARG ASN VAL ILE VAL SEQRES 21 A 316 ILE PRO LYS SER VAL THR PRO ALA ARG ILE VAL GLU ASN SEQRES 22 A 316 ILE GLN VAL PHE ASP PHE LYS LEU SER ASP GLU GLU MET SEQRES 23 A 316 ALA THR ILE LEU SER PHE ASN ARG ASN TRP ARG ALA CYS SEQRES 24 A 316 ASN LEU LEU GLN SER SER HIS LEU GLU ASP TYR PRO PHE SEQRES 25 A 316 ASN ALA GLU TYR HET NAP A 401 48 HET SBI A 402 17 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM SBI SORBINIL HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 SBI C11 H9 F N2 O3 FORMUL 4 HOH *336(H2 O) HELIX 1 1 LYS A 27 GLY A 39 1 13 HELIX 2 2 ALA A 46 GLN A 50 5 5 HELIX 3 3 ASN A 51 GLU A 65 1 15 HELIX 4 4 LYS A 69 LEU A 73 5 5 HELIX 5 5 TRP A 80 PHE A 84 5 5 HELIX 6 6 GLU A 85 LYS A 101 1 17 HELIX 7 7 THR A 137 GLU A 151 1 15 HELIX 8 8 SER A 163 ASN A 172 1 10 HELIX 9 9 GLN A 193 LYS A 203 1 11 HELIX 10 10 SER A 227 GLU A 230 5 4 HELIX 11 11 ASP A 231 HIS A 241 1 11 HELIX 12 12 THR A 244 GLN A 255 1 12 HELIX 13 13 THR A 266 GLN A 275 1 10 HELIX 14 14 SER A 282 SER A 291 1 10 HELIX 15 15 LEU A 301 SER A 305 5 5 HELIX 16 16 TYR A 310 ALA A 314 5 5 SHEET 1 A 2 PHE A 4 GLU A 6 0 SHEET 2 A 2 LYS A 12 PRO A 14 -1 O MET A 13 N VAL A 5 SHEET 1 B 8 GLY A 17 GLY A 19 0 SHEET 2 B 8 HIS A 42 ASP A 44 1 O ASP A 44 N LEU A 18 SHEET 3 B 8 PHE A 74 LEU A 79 1 O VAL A 76 N ILE A 43 SHEET 4 B 8 LEU A 105 ILE A 110 1 O LEU A 109 N LEU A 79 SHEET 5 B 8 VAL A 154 SER A 160 1 O LYS A 155 N LEU A 105 SHEET 6 B 8 THR A 182 GLU A 186 1 O THR A 182 N VAL A 159 SHEET 7 B 8 THR A 206 TYR A 210 1 O TYR A 210 N VAL A 185 SHEET 8 B 8 ILE A 259 VAL A 260 1 O ILE A 259 N ALA A 209 SITE 1 AC1 35 GLY A 19 THR A 20 TRP A 21 LYS A 22 SITE 2 AC1 35 ASP A 44 TYR A 49 HIS A 111 SER A 160 SITE 3 AC1 35 ASN A 161 GLN A 184 TYR A 210 SER A 211 SITE 4 AC1 35 PRO A 212 LEU A 213 GLY A 214 SER A 215 SITE 5 AC1 35 PRO A 216 ASP A 217 ALA A 246 ILE A 261 SITE 6 AC1 35 PRO A 262 LYS A 263 SER A 264 VAL A 265 SITE 7 AC1 35 THR A 266 ARG A 269 GLU A 272 ASN A 273 SITE 8 AC1 35 SBI A 402 HOH A 537 HOH A 561 HOH A 572 SITE 9 AC1 35 HOH A 601 HOH A 613 HOH A 683 SITE 1 AC2 11 TRP A 21 VAL A 48 TYR A 49 TRP A 80 SITE 2 AC2 11 HIS A 111 TRP A 112 PHE A 123 TRP A 220 SITE 3 AC2 11 LEU A 301 NAP A 401 HOH A 582 CRYST1 89.300 89.300 78.155 90.00 90.00 120.00 P 61 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 0.011198 0.006465 0.000000 0.00000 SCALE2 0.000000 0.012931 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012795 0.00000