HEADER OXIDOREDUCTASE 06-JAN-12 3VDQ TITLE CRYSTAL STRUCTURE OF ALCALIGENES FAECALIS D-3-HYDROXYBUTYRATE TITLE 2 DEHYDROGENASE IN COMPLEX WITH NAD(+) AND ACETATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-3-HYDROXYBUTYRATE DEHYDROGENASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 EC: 1.1.1.30 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALCALIGENES FAECALIS; SOURCE 3 ORGANISM_TAXID: 511 KEYWDS NAD DEPENDENT ENZYME, HYDROXYBUTYRATE DEHYDROGENASE, KETONE BODIES, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.M.HOQUE,S.SHIMIZU,M.T.HOSSAIN,T.YAMAMOTO,K.SUZUKI,A.TAKENAKA REVDAT 2 08-NOV-23 3VDQ 1 REMARK LINK REVDAT 1 29-FEB-12 3VDQ 0 SPRSDE 29-FEB-12 3VDQ 2ZEA JRNL AUTH M.M.HOQUE,S.SHIMIZU,M.T.HOSSAIN,T.YAMAMOTO,S.IMAMURA, JRNL AUTH 2 K.SUZUKI,M.TSUNODA,H.AMANO,T.SEKIGUCHI,A.TAKENAKA JRNL TITL THE STRUCTURES OF ALCALIGENES FAECALIS D-3-HYDROXYBUTYRATE JRNL TITL 2 DEHYDROGENASE BEFORE AND AFTER NAD+ AND ACETATE BINDING JRNL TITL 3 SUGGEST A DYNAMICAL REACTION MECHANISM AS A MEMBER OF THE JRNL TITL 4 SDR FAMILY. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 64 496 2008 JRNL REFN ISSN 0907-4449 JRNL PMID 18453685 JRNL DOI 10.1107/S0907444908004009 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 57435 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 5844 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7624 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 198 REMARK 3 SOLVENT ATOMS : 831 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) : 3.34400 REMARK 3 B22 (A**2) : 3.34400 REMARK 3 B33 (A**2) : -6.68900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.26 REMARK 3 LOW RESOLUTION CUTOFF (A) : 40.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ANISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3VDQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000069916. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-07 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : FLAT SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57443 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 46.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.47 REMARK 200 R MERGE (I) : 0.13300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.58 REMARK 200 R MERGE FOR SHELL (I) : 0.31700 REMARK 200 R SYM FOR SHELL (I) : 0.13040 REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.600 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: 2YZ7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.2M SODIUM ACETATE REMARK 280 TRIHYDRATE, 1.0M TRIS-HCL BUFFER, PH 8.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 131.04500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 45.70000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 65.52250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.70000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 45.70000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 196.56750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.70000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.70000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 65.52250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 45.70000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.70000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 196.56750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 131.04500 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 18210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -186.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 LEU A 84 107.44 -167.34 REMARK 500 ALA A 97 148.13 175.83 REMARK 500 LEU A 115 -60.28 -122.97 REMARK 500 ALA A 141 -120.39 -91.84 REMARK 500 SER A 142 164.56 176.25 REMARK 500 ALA B 62 129.53 -172.80 REMARK 500 ALA B 97 147.54 172.93 REMARK 500 LEU B 115 -63.68 -122.61 REMARK 500 ALA B 141 -119.38 -92.03 REMARK 500 SER B 142 166.11 171.57 REMARK 500 ARG B 189 72.81 -69.76 REMARK 500 ALA C 62 124.46 -179.19 REMARK 500 LEU C 64 0.81 -62.20 REMARK 500 LEU C 84 103.65 -160.19 REMARK 500 ALA C 91 131.34 -39.57 REMARK 500 ALA C 97 149.27 173.62 REMARK 500 LEU C 115 -60.11 -122.01 REMARK 500 ALA C 141 -116.64 -94.19 REMARK 500 SER C 142 172.18 174.70 REMARK 500 GLN C 203 -71.85 -50.04 REMARK 500 ALA D 62 124.50 172.47 REMARK 500 LEU D 84 105.96 -165.72 REMARK 500 ALA D 91 129.14 -39.58 REMARK 500 ALA D 97 149.43 -178.83 REMARK 500 LEU D 115 -61.83 -120.51 REMARK 500 ALA D 141 -118.43 -95.47 REMARK 500 SER D 142 171.80 175.95 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 CA C 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 260 OXT REMARK 620 2 HOH A 473 O 95.4 REMARK 620 3 ARG C 260 OXT 118.5 139.3 REMARK 620 4 HOH C 435 O 78.2 142.8 70.9 REMARK 620 5 HOH C 463 O 141.7 80.8 84.8 82.3 REMARK 620 6 HOH C 467 O 79.1 89.9 76.4 123.8 138.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG B 260 OXT REMARK 620 2 HOH B 451 O 80.3 REMARK 620 3 HOH B 482 O 83.0 86.2 REMARK 620 4 ARG D 260 OXT 133.9 77.8 134.6 REMARK 620 5 HOH D1001 O 79.6 125.2 140.0 80.9 REMARK 620 6 HOH D1053 O 130.4 141.7 77.3 89.5 87.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL C 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD C 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT D 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL D 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD D 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YZ7 RELATED DB: PDB REMARK 900 D-3-HYDROXYBUTYRATE DEHYDROGENASE IN NATIVE FORM REMARK 900 RELATED ID: 3VDR RELATED DB: PDB DBREF 3VDQ A 1 260 UNP D0VWQ0 D0VWQ0_ALCFA 1 260 DBREF 3VDQ B 1 260 UNP D0VWQ0 D0VWQ0_ALCFA 1 260 DBREF 3VDQ C 1 260 UNP D0VWQ0 D0VWQ0_ALCFA 1 260 DBREF 3VDQ D 1 260 UNP D0VWQ0 D0VWQ0_ALCFA 1 260 SEQRES 1 A 260 MET LEU LYS GLY LYS LYS ALA VAL VAL THR GLY SER THR SEQRES 2 A 260 SER GLY ILE GLY LEU ALA MET ALA THR GLU LEU ALA LYS SEQRES 3 A 260 ALA GLY ALA ASP VAL VAL ILE ASN GLY PHE GLY GLN PRO SEQRES 4 A 260 GLU ASP ILE GLU ARG GLU ARG SER THR LEU GLU SER LYS SEQRES 5 A 260 PHE GLY VAL LYS ALA TYR TYR LEU ASN ALA ASP LEU SER SEQRES 6 A 260 ASP ALA GLN ALA THR ARG ASP PHE ILE ALA LYS ALA ALA SEQRES 7 A 260 GLU ALA LEU GLY GLY LEU ASP ILE LEU VAL ASN ASN ALA SEQRES 8 A 260 GLY ILE GLN HIS THR ALA PRO ILE GLU GLU PHE PRO VAL SEQRES 9 A 260 ASP LYS TRP ASN ALA ILE ILE ALA LEU ASN LEU SER ALA SEQRES 10 A 260 VAL PHE HIS GLY THR ALA ALA ALA LEU PRO ILE MET GLN SEQRES 11 A 260 LYS GLN GLY TRP GLY ARG ILE ILE ASN ILE ALA SER ALA SEQRES 12 A 260 HIS GLY LEU VAL ALA SER VAL ASN LYS SER ALA TYR VAL SEQRES 13 A 260 ALA ALA LYS HIS GLY VAL VAL GLY LEU THR LYS VAL THR SEQRES 14 A 260 ALA LEU GLU ASN ALA GLY LYS GLY ILE THR CYS ASN ALA SEQRES 15 A 260 ILE CYS PRO GLY TRP VAL ARG THR PRO LEU VAL GLU LYS SEQRES 16 A 260 GLN ILE GLU ALA ILE SER GLN GLN LYS GLY ILE ASP ILE SEQRES 17 A 260 GLU ALA ALA ALA ARG GLU LEU LEU ALA GLU LYS GLN PRO SEQRES 18 A 260 SER LEU GLN PHE VAL THR PRO GLU GLN LEU GLY GLY ALA SEQRES 19 A 260 ALA VAL PHE LEU SER SER ALA ALA ALA ASP GLN MET THR SEQRES 20 A 260 GLY THR THR LEU SER LEU ASP GLY GLY TRP THR ALA ARG SEQRES 1 B 260 MET LEU LYS GLY LYS LYS ALA VAL VAL THR GLY SER THR SEQRES 2 B 260 SER GLY ILE GLY LEU ALA MET ALA THR GLU LEU ALA LYS SEQRES 3 B 260 ALA GLY ALA ASP VAL VAL ILE ASN GLY PHE GLY GLN PRO SEQRES 4 B 260 GLU ASP ILE GLU ARG GLU ARG SER THR LEU GLU SER LYS SEQRES 5 B 260 PHE GLY VAL LYS ALA TYR TYR LEU ASN ALA ASP LEU SER SEQRES 6 B 260 ASP ALA GLN ALA THR ARG ASP PHE ILE ALA LYS ALA ALA SEQRES 7 B 260 GLU ALA LEU GLY GLY LEU ASP ILE LEU VAL ASN ASN ALA SEQRES 8 B 260 GLY ILE GLN HIS THR ALA PRO ILE GLU GLU PHE PRO VAL SEQRES 9 B 260 ASP LYS TRP ASN ALA ILE ILE ALA LEU ASN LEU SER ALA SEQRES 10 B 260 VAL PHE HIS GLY THR ALA ALA ALA LEU PRO ILE MET GLN SEQRES 11 B 260 LYS GLN GLY TRP GLY ARG ILE ILE ASN ILE ALA SER ALA SEQRES 12 B 260 HIS GLY LEU VAL ALA SER VAL ASN LYS SER ALA TYR VAL SEQRES 13 B 260 ALA ALA LYS HIS GLY VAL VAL GLY LEU THR LYS VAL THR SEQRES 14 B 260 ALA LEU GLU ASN ALA GLY LYS GLY ILE THR CYS ASN ALA SEQRES 15 B 260 ILE CYS PRO GLY TRP VAL ARG THR PRO LEU VAL GLU LYS SEQRES 16 B 260 GLN ILE GLU ALA ILE SER GLN GLN LYS GLY ILE ASP ILE SEQRES 17 B 260 GLU ALA ALA ALA ARG GLU LEU LEU ALA GLU LYS GLN PRO SEQRES 18 B 260 SER LEU GLN PHE VAL THR PRO GLU GLN LEU GLY GLY ALA SEQRES 19 B 260 ALA VAL PHE LEU SER SER ALA ALA ALA ASP GLN MET THR SEQRES 20 B 260 GLY THR THR LEU SER LEU ASP GLY GLY TRP THR ALA ARG SEQRES 1 C 260 MET LEU LYS GLY LYS LYS ALA VAL VAL THR GLY SER THR SEQRES 2 C 260 SER GLY ILE GLY LEU ALA MET ALA THR GLU LEU ALA LYS SEQRES 3 C 260 ALA GLY ALA ASP VAL VAL ILE ASN GLY PHE GLY GLN PRO SEQRES 4 C 260 GLU ASP ILE GLU ARG GLU ARG SER THR LEU GLU SER LYS SEQRES 5 C 260 PHE GLY VAL LYS ALA TYR TYR LEU ASN ALA ASP LEU SER SEQRES 6 C 260 ASP ALA GLN ALA THR ARG ASP PHE ILE ALA LYS ALA ALA SEQRES 7 C 260 GLU ALA LEU GLY GLY LEU ASP ILE LEU VAL ASN ASN ALA SEQRES 8 C 260 GLY ILE GLN HIS THR ALA PRO ILE GLU GLU PHE PRO VAL SEQRES 9 C 260 ASP LYS TRP ASN ALA ILE ILE ALA LEU ASN LEU SER ALA SEQRES 10 C 260 VAL PHE HIS GLY THR ALA ALA ALA LEU PRO ILE MET GLN SEQRES 11 C 260 LYS GLN GLY TRP GLY ARG ILE ILE ASN ILE ALA SER ALA SEQRES 12 C 260 HIS GLY LEU VAL ALA SER VAL ASN LYS SER ALA TYR VAL SEQRES 13 C 260 ALA ALA LYS HIS GLY VAL VAL GLY LEU THR LYS VAL THR SEQRES 14 C 260 ALA LEU GLU ASN ALA GLY LYS GLY ILE THR CYS ASN ALA SEQRES 15 C 260 ILE CYS PRO GLY TRP VAL ARG THR PRO LEU VAL GLU LYS SEQRES 16 C 260 GLN ILE GLU ALA ILE SER GLN GLN LYS GLY ILE ASP ILE SEQRES 17 C 260 GLU ALA ALA ALA ARG GLU LEU LEU ALA GLU LYS GLN PRO SEQRES 18 C 260 SER LEU GLN PHE VAL THR PRO GLU GLN LEU GLY GLY ALA SEQRES 19 C 260 ALA VAL PHE LEU SER SER ALA ALA ALA ASP GLN MET THR SEQRES 20 C 260 GLY THR THR LEU SER LEU ASP GLY GLY TRP THR ALA ARG SEQRES 1 D 260 MET LEU LYS GLY LYS LYS ALA VAL VAL THR GLY SER THR SEQRES 2 D 260 SER GLY ILE GLY LEU ALA MET ALA THR GLU LEU ALA LYS SEQRES 3 D 260 ALA GLY ALA ASP VAL VAL ILE ASN GLY PHE GLY GLN PRO SEQRES 4 D 260 GLU ASP ILE GLU ARG GLU ARG SER THR LEU GLU SER LYS SEQRES 5 D 260 PHE GLY VAL LYS ALA TYR TYR LEU ASN ALA ASP LEU SER SEQRES 6 D 260 ASP ALA GLN ALA THR ARG ASP PHE ILE ALA LYS ALA ALA SEQRES 7 D 260 GLU ALA LEU GLY GLY LEU ASP ILE LEU VAL ASN ASN ALA SEQRES 8 D 260 GLY ILE GLN HIS THR ALA PRO ILE GLU GLU PHE PRO VAL SEQRES 9 D 260 ASP LYS TRP ASN ALA ILE ILE ALA LEU ASN LEU SER ALA SEQRES 10 D 260 VAL PHE HIS GLY THR ALA ALA ALA LEU PRO ILE MET GLN SEQRES 11 D 260 LYS GLN GLY TRP GLY ARG ILE ILE ASN ILE ALA SER ALA SEQRES 12 D 260 HIS GLY LEU VAL ALA SER VAL ASN LYS SER ALA TYR VAL SEQRES 13 D 260 ALA ALA LYS HIS GLY VAL VAL GLY LEU THR LYS VAL THR SEQRES 14 D 260 ALA LEU GLU ASN ALA GLY LYS GLY ILE THR CYS ASN ALA SEQRES 15 D 260 ILE CYS PRO GLY TRP VAL ARG THR PRO LEU VAL GLU LYS SEQRES 16 D 260 GLN ILE GLU ALA ILE SER GLN GLN LYS GLY ILE ASP ILE SEQRES 17 D 260 GLU ALA ALA ALA ARG GLU LEU LEU ALA GLU LYS GLN PRO SEQRES 18 D 260 SER LEU GLN PHE VAL THR PRO GLU GLN LEU GLY GLY ALA SEQRES 19 D 260 ALA VAL PHE LEU SER SER ALA ALA ALA ASP GLN MET THR SEQRES 20 D 260 GLY THR THR LEU SER LEU ASP GLY GLY TRP THR ALA ARG HET ACT A 301 4 HET CL A 302 1 HET NAD A 303 44 HET ACT B 301 4 HET CL B 302 1 HET NAD B 303 44 HET CA B 304 1 HET CA C 301 1 HET ACT C 302 4 HET CL C 303 1 HET NAD C 304 44 HET ACT D 301 4 HET CL D 302 1 HET NAD D 303 44 HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM CA CALCIUM ION FORMUL 5 ACT 4(C2 H3 O2 1-) FORMUL 6 CL 4(CL 1-) FORMUL 7 NAD 4(C21 H27 N7 O14 P2) FORMUL 11 CA 2(CA 2+) FORMUL 19 HOH *831(H2 O) HELIX 1 1 SER A 14 ALA A 27 1 14 HELIX 2 2 GLN A 38 GLY A 54 1 17 HELIX 3 3 ASP A 66 GLY A 82 1 17 HELIX 4 4 PRO A 98 PHE A 102 5 5 HELIX 5 5 PRO A 103 LEU A 115 1 13 HELIX 6 6 LEU A 115 GLY A 133 1 19 HELIX 7 7 SER A 142 LEU A 146 5 5 HELIX 8 8 LYS A 152 ASN A 173 1 22 HELIX 9 9 THR A 190 GLY A 205 1 16 HELIX 10 10 ASP A 207 GLN A 220 1 14 HELIX 11 11 THR A 227 SER A 239 1 13 HELIX 12 12 SER A 240 ASP A 244 5 5 HELIX 13 13 GLY A 256 ARG A 260 5 5 HELIX 14 14 SER B 14 ALA B 27 1 14 HELIX 15 15 GLN B 38 GLY B 54 1 17 HELIX 16 16 ASP B 66 GLY B 82 1 17 HELIX 17 17 PRO B 98 PHE B 102 5 5 HELIX 18 18 PRO B 103 LEU B 115 1 13 HELIX 19 19 LEU B 115 GLY B 133 1 19 HELIX 20 20 SER B 142 LEU B 146 5 5 HELIX 21 21 LYS B 152 ASN B 173 1 22 HELIX 22 22 THR B 190 LYS B 204 1 15 HELIX 23 23 ASP B 207 GLN B 220 1 14 HELIX 24 24 THR B 227 SER B 239 1 13 HELIX 25 25 SER B 240 ASP B 244 5 5 HELIX 26 26 GLY B 256 ARG B 260 5 5 HELIX 27 27 SER C 14 ALA C 27 1 14 HELIX 28 28 GLN C 38 GLY C 54 1 17 HELIX 29 29 ASP C 66 GLY C 82 1 17 HELIX 30 30 PRO C 98 PHE C 102 5 5 HELIX 31 31 PRO C 103 LEU C 115 1 13 HELIX 32 32 LEU C 115 GLY C 133 1 19 HELIX 33 33 SER C 142 LEU C 146 5 5 HELIX 34 34 LYS C 152 ASN C 173 1 22 HELIX 35 35 THR C 190 LYS C 204 1 15 HELIX 36 36 ASP C 207 GLN C 220 1 14 HELIX 37 37 THR C 227 SER C 240 1 14 HELIX 38 38 ALA C 241 ASP C 244 5 4 HELIX 39 39 GLY C 256 ARG C 260 5 5 HELIX 40 40 SER D 14 ALA D 27 1 14 HELIX 41 41 GLN D 38 GLY D 54 1 17 HELIX 42 42 ASP D 66 GLY D 82 1 17 HELIX 43 43 PRO D 98 PHE D 102 5 5 HELIX 44 44 PRO D 103 LEU D 115 1 13 HELIX 45 45 LEU D 115 GLY D 133 1 19 HELIX 46 46 SER D 142 LEU D 146 5 5 HELIX 47 47 LYS D 152 ASN D 173 1 22 HELIX 48 48 THR D 190 LYS D 204 1 15 HELIX 49 49 ASP D 207 GLN D 220 1 14 HELIX 50 50 THR D 227 SER D 239 1 13 HELIX 51 51 SER D 240 ASP D 244 5 5 HELIX 52 52 GLY D 256 ARG D 260 5 5 SHEET 1 A 7 ALA A 57 TYR A 59 0 SHEET 2 A 7 ASP A 30 ILE A 33 1 N ILE A 33 O TYR A 58 SHEET 3 A 7 LYS A 6 VAL A 9 1 N ALA A 7 O ASP A 30 SHEET 4 A 7 ILE A 86 ASN A 89 1 O VAL A 88 N VAL A 8 SHEET 5 A 7 GLY A 135 ILE A 140 1 O ILE A 138 N LEU A 87 SHEET 6 A 7 ILE A 178 PRO A 185 1 O ILE A 183 N ASN A 139 SHEET 7 A 7 THR A 250 LEU A 253 1 O LEU A 251 N ALA A 182 SHEET 1 B 7 ALA B 57 TYR B 59 0 SHEET 2 B 7 ASP B 30 ILE B 33 1 N ILE B 33 O TYR B 58 SHEET 3 B 7 LYS B 6 VAL B 9 1 N ALA B 7 O ASP B 30 SHEET 4 B 7 ILE B 86 ASN B 89 1 O VAL B 88 N VAL B 8 SHEET 5 B 7 GLY B 135 ILE B 140 1 O ILE B 138 N LEU B 87 SHEET 6 B 7 ILE B 178 PRO B 185 1 O ILE B 183 N ASN B 139 SHEET 7 B 7 THR B 250 LEU B 253 1 O LEU B 251 N ALA B 182 SHEET 1 C 7 ALA C 57 TYR C 59 0 SHEET 2 C 7 ASP C 30 ILE C 33 1 N ILE C 33 O TYR C 58 SHEET 3 C 7 LYS C 6 VAL C 9 1 N ALA C 7 O ASP C 30 SHEET 4 C 7 ILE C 86 ASN C 89 1 O VAL C 88 N VAL C 8 SHEET 5 C 7 GLY C 135 ILE C 140 1 O ILE C 138 N LEU C 87 SHEET 6 C 7 ILE C 178 PRO C 185 1 O ASN C 181 N ASN C 139 SHEET 7 C 7 THR C 250 LEU C 253 1 O LEU C 251 N CYS C 184 SHEET 1 D 7 ALA D 57 TYR D 59 0 SHEET 2 D 7 ASP D 30 ILE D 33 1 N ILE D 33 O TYR D 58 SHEET 3 D 7 LYS D 6 VAL D 9 1 N ALA D 7 O ASP D 30 SHEET 4 D 7 ILE D 86 ASN D 89 1 O VAL D 88 N VAL D 8 SHEET 5 D 7 GLY D 135 ILE D 140 1 O ILE D 138 N LEU D 87 SHEET 6 D 7 ILE D 178 PRO D 185 1 O ASN D 181 N ASN D 139 SHEET 7 D 7 THR D 250 LEU D 253 1 O LEU D 251 N ALA D 182 LINK OXT ARG A 260 CA CA C 301 1555 1555 2.50 LINK O HOH A 473 CA CA C 301 1555 1555 2.58 LINK OXT ARG B 260 CA CA B 304 1555 1555 2.44 LINK CA CA B 304 O HOH B 451 1555 1555 2.56 LINK CA CA B 304 O HOH B 482 1555 1555 2.53 LINK CA CA B 304 OXT ARG D 260 1555 1555 2.46 LINK CA CA B 304 O HOH D1001 1555 1555 2.65 LINK CA CA B 304 O HOH D1053 1555 1555 2.58 LINK OXT ARG C 260 CA CA C 301 1555 1555 2.53 LINK CA CA C 301 O HOH C 435 1555 1555 2.65 LINK CA CA C 301 O HOH C 463 1555 1555 2.53 LINK CA CA C 301 O HOH C 467 1555 1555 2.64 SITE 1 AC1 7 GLN A 94 HIS A 144 LYS A 152 TRP A 187 SITE 2 AC1 7 LEU A 192 GLN A 196 HOH A 403 SITE 1 AC2 3 SER A 149 VAL A 150 LYS A 219 SITE 1 AC3 30 GLY A 11 THR A 13 SER A 14 ILE A 16 SITE 2 AC3 30 PHE A 36 ASP A 63 LEU A 64 ASN A 90 SITE 3 AC3 30 ALA A 91 GLY A 92 LEU A 113 ILE A 140 SITE 4 AC3 30 ALA A 141 SER A 142 TYR A 155 LYS A 159 SITE 5 AC3 30 PRO A 185 GLY A 186 TRP A 187 VAL A 188 SITE 6 AC3 30 THR A 190 PRO A 191 LEU A 192 VAL A 193 SITE 7 AC3 30 HOH A 402 HOH A 403 HOH A 465 HOH A 596 SITE 8 AC3 30 HOH C 486 HOH C 603 SITE 1 AC4 8 GLN B 94 HIS B 144 LYS B 152 TRP B 187 SITE 2 AC4 8 LEU B 192 GLN B 196 NAD B 303 HOH B 517 SITE 1 AC5 3 SER B 149 VAL B 150 LYS B 219 SITE 1 AC6 33 GLY B 11 THR B 13 SER B 14 GLY B 15 SITE 2 AC6 33 ILE B 16 ASN B 34 PHE B 36 ASP B 63 SITE 3 AC6 33 LEU B 64 ASN B 90 ALA B 91 GLY B 92 SITE 4 AC6 33 ILE B 140 ALA B 141 SER B 142 TYR B 155 SITE 5 AC6 33 LYS B 159 PRO B 185 GLY B 186 TRP B 187 SITE 6 AC6 33 VAL B 188 THR B 190 PRO B 191 LEU B 192 SITE 7 AC6 33 VAL B 193 ACT B 301 HOH B 405 HOH B 474 SITE 8 AC6 33 HOH B 517 HOH B 531 HOH B 544 HOH B 548 SITE 9 AC6 33 HOH B 553 SITE 1 AC7 6 ARG B 260 HOH B 451 HOH B 482 ARG D 260 SITE 2 AC7 6 HOH D1001 HOH D1053 SITE 1 AC8 7 VAL A 147 ARG A 260 HOH A 473 ARG C 260 SITE 2 AC8 7 HOH C 435 HOH C 463 HOH C 467 SITE 1 AC9 8 GLN C 94 HIS C 144 LYS C 152 TRP C 187 SITE 2 AC9 8 LEU C 192 GLN C 196 NAD C 304 HOH C 459 SITE 1 BC1 3 SER C 149 VAL C 150 LYS C 219 SITE 1 BC2 31 HOH A 534 GLY C 11 THR C 13 SER C 14 SITE 2 BC2 31 ILE C 16 PHE C 36 ASP C 63 LEU C 64 SITE 3 BC2 31 ASN C 90 ALA C 91 GLY C 92 LEU C 113 SITE 4 BC2 31 ILE C 140 ALA C 141 SER C 142 TYR C 155 SITE 5 BC2 31 LYS C 159 PRO C 185 GLY C 186 TRP C 187 SITE 6 BC2 31 VAL C 188 THR C 190 PRO C 191 LEU C 192 SITE 7 BC2 31 VAL C 193 ACT C 302 HOH C 441 HOH C 510 SITE 8 BC2 31 HOH C 598 HOH C 599 HOH C 602 SITE 1 BC3 6 GLN D 94 HIS D 144 LYS D 152 TRP D 187 SITE 2 BC3 6 GLN D 196 HOH D1019 SITE 1 BC4 3 SER D 149 VAL D 150 LYS D 219 SITE 1 BC5 30 GLY D 11 THR D 13 SER D 14 GLY D 15 SITE 2 BC5 30 ILE D 16 ASN D 34 PHE D 36 ASP D 63 SITE 3 BC5 30 LEU D 64 ASN D 90 ALA D 91 GLY D 92 SITE 4 BC5 30 ILE D 140 ALA D 141 TYR D 155 LYS D 159 SITE 5 BC5 30 PRO D 185 GLY D 186 TRP D 187 VAL D 188 SITE 6 BC5 30 THR D 190 PRO D 191 LEU D 192 VAL D 193 SITE 7 BC5 30 HOH D1019 HOH D1117 HOH D1126 HOH D1187 SITE 8 BC5 30 HOH D1188 HOH D1195 CRYST1 91.400 91.400 262.090 90.00 90.00 90.00 P 41 21 2 32 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 0.010941 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010941 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003815 0.00000