HEADER OXIDOREDUCTASE 30-OCT-24 9KBB TITLE 3-HYDROXYISOBUTYRATE DEHYDROGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-HYDROXYISOBUTYRATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MICROMONOSPORA ECHINAURANTIACA; SOURCE 3 ORGANISM_TAXID: 47857; SOURCE 4 GENE: GA0070609_2033; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE ACTIVITY, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.FANG,Z.LIU REVDAT 3 03-DEC-25 9KBB 1 JRNL REVDAT 2 06-AUG-25 9KBB 1 JRNL REVDAT 1 30-JUL-25 9KBB 0 JRNL AUTH K.LI,Z.LIU,B.WANG,L.HUANG,L.YU,Z.ZHOU,L.LIN,P.FANG,H.FU JRNL TITL IMINE REDUCTASE-CATALYZED REMOTE STEREOCONTROL FOR JRNL TITL 2 ENANTIODIVERGENT SYNTHESIS OF CYCLOHEXYLIDENE-BASED AXIALLY JRNL TITL 3 CHIRAL AMINES. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 64 00572 2025 JRNL REFN ESSN 1521-3773 JRNL PMID 40393926 JRNL DOI 10.1002/ANIE.202500572 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 25.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 18825 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1902 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 25.8600 - 4.3000 0.99 1731 197 0.1685 0.1766 REMARK 3 2 4.3000 - 3.4200 1.00 1691 193 0.1772 0.1908 REMARK 3 3 3.4200 - 2.9900 1.00 1712 193 0.2026 0.2166 REMARK 3 4 2.9900 - 2.7100 1.00 1675 184 0.2052 0.2489 REMARK 3 5 2.7100 - 2.5200 1.00 1710 187 0.2097 0.2022 REMARK 3 6 2.5200 - 2.3700 1.00 1675 189 0.2010 0.2775 REMARK 3 7 2.3700 - 2.2500 1.00 1675 196 0.2089 0.2169 REMARK 3 8 2.2500 - 2.1500 1.00 1706 187 0.2024 0.2603 REMARK 3 9 2.1500 - 2.0700 1.00 1681 186 0.2165 0.2391 REMARK 3 10 2.0700 - 2.0000 1.00 1667 190 0.2269 0.2633 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 21.630 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 : 0.004 2093 REMARK 3 ANGLE : 0.685 2869 REMARK 3 CHIRALITY : 0.038 340 REMARK 3 PLANARITY : 0.015 374 REMARK 3 DIHEDRAL : 7.762 315 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 9KBB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 17-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300053209. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-SEP-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 0.97853 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18833 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 47.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.5000 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) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.06700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 21.20 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA2HPO4,K2HPO4,BISTRIS,PEG 3350, PH REMARK 280 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 37.63950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.82600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 37.63950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.82600 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -94.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 636 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 643 LIES ON A SPECIAL POSITION. 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 233 32.67 -98.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 41 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF1 9KBB A 7 291 UNP A0A1C5HQ65_9ACTN DBREF2 9KBB A A0A1C5HQ65 7 291 SEQRES 1 A 285 ARG PRO VAL THR VAL LEU GLY LEU GLY ALA MET GLY ARG SEQRES 2 A 285 ALA LEU ALA GLY ALA LEU VAL ALA ALA GLY HIS PRO THR SEQRES 3 A 285 THR VAL TRP ASN ARG THR PRO GLY ARG ALA ALA ALA LEU SEQRES 4 A 285 THR ALA ALA GLY ALA THR GLU ALA GLY THR ALA ALA GLU SEQRES 5 A 285 ALA VAL ALA ALA GLY ASP LEU VAL VAL VAL CYS LEU LEU SEQRES 6 A 285 ASP ASP GLU VAL THR ARG GLN VAL LEU ALA LEU VAL ALA SEQRES 7 A 285 PRO VAL LEU ALA GLY ARG THR LEU VAL ASN LEU THR ASN SEQRES 8 A 285 GLY THR PRO GLU GLN ALA ARG ARG LEU ALA GLU TRP ALA SEQRES 9 A 285 THR SER HIS GLY ALA ASP HIS LEU ASP GLY GLY ILE MET SEQRES 10 A 285 ALA VAL PRO ALA MET ILE GLY GLN PRO GLY ALA LEU ILE SEQRES 11 A 285 LEU TYR SER GLY PRO GLU ASP VAL PHE ARG ALA GLY ARG SEQRES 12 A 285 GLU THR LEU ALA ALA PHE GLY ALA ALA HIS TRP LEU GLY SEQRES 13 A 285 ALA ASP PRO GLY ALA ALA ALA LEU HIS ASP LEU ALA LEU SEQRES 14 A 285 LEU ALA ALA MET TYR GLY MET PHE GLY GLY TYR LEU HIS SEQRES 15 A 285 ALA VAL ALA MET ILE ARG ALA ALA GLY VAL PRO ALA THR SEQRES 16 A 285 GLY PHE THR PRO LEU ALA THR ASP TRP LEU THR ALA MET SEQRES 17 A 285 LEU GLY ALA LEU PRO ALA LEU ALA ARG GLY VAL ASP SER SEQRES 18 A 285 GLY ASP HIS ALA ALA ASP GLY SER ALA VAL GLY MET GLN SEQRES 19 A 285 ALA ALA ALA PHE GLY ASN LEU LEU ALA ALA SER ARG GLU SEQRES 20 A 285 GLY GLY VAL SER THR SER LEU LEU GLU PRO VAL ARG ARG SEQRES 21 A 285 LEU LEU ASP ASP ALA VAL ARG ALA GLY HIS GLY ALA ASP SEQRES 22 A 285 GLY LEU SER ALA LEU VAL ASP LEU LEU ARG GLN SER HET NAP A 301 48 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 HOH *251(H2 O) HELIX 1 AA1 GLY A 15 GLY A 29 1 15 HELIX 2 AA2 ALA A 42 ALA A 48 1 7 HELIX 3 AA3 THR A 55 ALA A 62 1 8 HELIX 4 AA4 ASP A 72 ALA A 84 1 13 HELIX 5 AA5 PRO A 85 LEU A 87 5 3 HELIX 6 AA6 THR A 99 HIS A 113 1 15 HELIX 7 AA7 VAL A 125 ILE A 129 5 5 HELIX 8 AA8 PRO A 141 ALA A 153 1 13 HELIX 9 AA9 ALA A 154 GLY A 156 5 3 HELIX 10 AB1 GLY A 166 ALA A 196 1 31 HELIX 11 AB2 PRO A 199 GLY A 216 1 18 HELIX 12 AB3 ALA A 217 GLY A 228 1 12 HELIX 13 AB4 ALA A 236 GLY A 254 1 19 HELIX 14 AB5 LEU A 261 ALA A 274 1 14 HELIX 15 AB6 GLY A 280 ARG A 289 5 10 SHEET 1 AA1 8 THR A 51 GLU A 52 0 SHEET 2 AA1 8 THR A 32 TRP A 35 1 N VAL A 34 O THR A 51 SHEET 3 AA1 8 VAL A 9 LEU A 12 1 N VAL A 9 O THR A 33 SHEET 4 AA1 8 LEU A 65 VAL A 68 1 O VAL A 67 N THR A 10 SHEET 5 AA1 8 THR A 91 ASN A 94 1 O THR A 91 N VAL A 66 SHEET 6 AA1 8 ASP A 116 ILE A 122 1 O LEU A 118 N LEU A 92 SHEET 7 AA1 8 LEU A 135 SER A 139 -1 O LEU A 137 N GLY A 121 SHEET 8 AA1 8 ALA A 157 TRP A 160 1 O HIS A 159 N TYR A 138 CRYST1 75.279 61.652 60.634 90.00 92.21 90.00 C 1 2 1 4 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 0.013284 0.000000 0.000513 0.00000 SCALE2 0.000000 0.016220 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016505 0.00000 CONECT 2007 2008 2009 2010 2029 CONECT 2008 2007 CONECT 2009 2007 CONECT 2010 2007 2011 CONECT 2011 2010 2012 CONECT 2012 2011 2013 2014 CONECT 2013 2012 2018 CONECT 2014 2012 2015 2016 CONECT 2015 2014 CONECT 2016 2014 2017 2018 CONECT 2017 2016 2051 CONECT 2018 2013 2016 2019 CONECT 2019 2018 2020 2028 CONECT 2020 2019 2021 CONECT 2021 2020 2022 CONECT 2022 2021 2023 2028 CONECT 2023 2022 2024 2025 CONECT 2024 2023 CONECT 2025 2023 2026 CONECT 2026 2025 2027 CONECT 2027 2026 2028 CONECT 2028 2019 2022 2027 CONECT 2029 2007 2030 CONECT 2030 2029 2031 2032 2033 CONECT 2031 2030 CONECT 2032 2030 CONECT 2033 2030 2034 CONECT 2034 2033 2035 CONECT 2035 2034 2036 2037 CONECT 2036 2035 2041 CONECT 2037 2035 2038 2039 CONECT 2038 2037 CONECT 2039 2037 2040 2041 CONECT 2040 2039 CONECT 2041 2036 2039 2042 CONECT 2042 2041 2043 2050 CONECT 2043 2042 2044 CONECT 2044 2043 2045 2048 CONECT 2045 2044 2046 2047 CONECT 2046 2045 CONECT 2047 2045 CONECT 2048 2044 2049 CONECT 2049 2048 2050 CONECT 2050 2042 2049 CONECT 2051 2017 2052 2053 2054 CONECT 2052 2051 CONECT 2053 2051 CONECT 2054 2051 MASTER 247 0 1 15 8 0 0 6 2304 1 48 22 END