HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 12-MAR-13 3W8F TITLE CRYSTAL STRUCTURE OF D-3-HYDROXYBUTYRATE DEHYDROGENASE FROM TITLE 2 ALCALIGENES FAECALIS COMPLEXED WITH NAD+ AND AN INHIBITOR MALONATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-3-HYDROXYBUTYRATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.1.30; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALCALIGENES FAECALIS; SOURCE 3 ORGANISM_TAXID: 511; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS ROSSMANN FOLD, OXIDREDUCTASE, NAD+ BINDING, MALONATE BINDING, KEYWDS 2 MITOCHONDRIA, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.KANAZAWA,M.TSUNODA,M.M.HOQUE,K.SUZUKI,T.YAMAMOTO,A.TAKENAKA REVDAT 3 08-NOV-23 3W8F 1 REMARK LINK REVDAT 2 29-APR-15 3W8F 1 HETSYN REVDAT 1 12-MAR-14 3W8F 0 JRNL AUTH H.KANAZAWA,M.TSUNODA,M.M.HOQUE,K.SUZUKI,T.YAMAMOTO, JRNL AUTH 2 A.TAKENAKA JRNL TITL X-RAY DIFFRACTION OF D-3-HYDROXYBUTYRATE DEHYDROGENASE FROM JRNL TITL 2 ALCALIGENES FAECALIS COMPLEXED WITH NAD+ AND MALONATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 41170 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 + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 4182 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2806 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.1360 REMARK 3 BIN FREE R VALUE SET COUNT : 317 REMARK 3 BIN FREE R VALUE : 0.1710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1906 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 331 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.061 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.063 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.031 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.760 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2042 ; 0.027 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2796 ; 2.367 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 279 ; 6.186 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 73 ;38.212 ;25.616 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 336 ;12.960 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ; 9.303 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 333 ; 0.148 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1509 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1317 ; 1.281 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2110 ; 2.104 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 725 ; 3.301 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 676 ; 5.458 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3W8F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000096016. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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-5A 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 : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42260 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.990 REMARK 200 RESOLUTION RANGE LOW (A) : 22.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: 3VDR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 32% PEG4000, 100MM TRIS HYDROCHLORIDE, REMARK 280 200MM MALONATE, 5MM NAD+, PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 31.41500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.41500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.64500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.41500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.41500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 59.64500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.41500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.41500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 59.64500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.41500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.41500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 59.64500 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 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 18410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -219.0 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 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 NA NA A 303 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 611 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 674 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 534 O HOH A 720 2.00 REMARK 500 O HOH A 524 O HOH A 652 2.02 REMARK 500 O HOH A 703 O HOH A 720 2.02 REMARK 500 O HOH A 444 O HOH A 637 2.14 REMARK 500 O HOH A 592 O HOH A 677 2.14 REMARK 500 O HOH A 502 O HOH A 652 2.16 REMARK 500 O HOH A 590 O HOH A 691 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 717 O HOH A 717 2455 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 45 CD GLU A 45 OE2 0.079 REMARK 500 GLU A 229 CD GLU A 229 OE1 0.074 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 46 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 71 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 71 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 136 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 189 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP A 244 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 84 107.13 -161.29 REMARK 500 ALA A 141 -120.10 -93.35 REMARK 500 SER A 142 160.52 177.19 REMARK 500 ASP A 254 14.31 -146.75 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 NA A 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 260 OXT REMARK 620 2 HOH A 434 O 88.2 REMARK 620 3 HOH A 454 O 79.0 143.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3W8D RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH NAD+ AND METHYLMALONATE. REMARK 900 RELATED ID: 3W8E RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH NAD+ AND D-3-HYDROXYBUTYRATE, AND REMARK 900 HIGH RESOLUTION. REMARK 900 RELATED ID: 3VDR RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH NAD+ AND D-3-HYDROXYBUTYRATE. REMARK 900 RELATED ID: 2YZ7 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN NATIVE FORM. REMARK 900 RELATED ID: 3VDQ RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH NAD+ AND ACETATE. DBREF 3W8F A 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 HET NAD A 301 44 HET MLA A 302 7 HET NA A 303 1 HET CL A 304 1 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM MLA MALONIC ACID HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETSYN MLA DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; HETSYN 2 MLA METHANEDICARBOXYLIC ACID FORMUL 2 NAD C21 H27 N7 O14 P2 FORMUL 3 MLA C3 H4 O4 FORMUL 4 NA NA 1+ FORMUL 5 CL CL 1- FORMUL 6 HOH *331(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 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 ASN A 181 N ASN A 139 SHEET 7 A 7 THR A 250 LEU A 253 1 O LEU A 251 N CYS A 184 LINK OXT ARG A 260 NA NA A 303 1555 1555 2.35 LINK NA NA A 303 O HOH A 434 1555 1555 2.32 LINK NA NA A 303 O HOH A 454 1555 1555 2.39 SITE 1 AC1 34 GLY A 11 THR A 13 SER A 14 GLY A 15 SITE 2 AC1 34 ILE A 16 ASN A 34 PHE A 36 ALA A 62 SITE 3 AC1 34 ASP A 63 LEU A 64 ASN A 90 ALA A 91 SITE 4 AC1 34 GLY A 92 LEU A 113 ILE A 140 ALA A 141 SITE 5 AC1 34 SER A 142 TYR A 155 LYS A 159 PRO A 185 SITE 6 AC1 34 GLY A 186 TRP A 187 VAL A 188 THR A 190 SITE 7 AC1 34 PRO A 191 LEU A 192 VAL A 193 MLA A 302 SITE 8 AC1 34 HOH A 402 HOH A 421 HOH A 522 HOH A 526 SITE 9 AC1 34 HOH A 638 HOH A 667 SITE 1 AC2 9 GLN A 94 SER A 142 HIS A 144 LYS A 152 SITE 2 AC2 9 TYR A 155 LEU A 192 GLN A 196 NAD A 301 SITE 3 AC2 9 HOH A 560 SITE 1 AC3 3 ARG A 260 HOH A 434 HOH A 454 SITE 1 AC4 4 SER A 149 VAL A 150 LYS A 219 HOH A 441 CRYST1 62.830 62.830 119.290 90.00 90.00 90.00 P 42 21 2 8 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 0.015916 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015916 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008383 0.00000