HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 12-MAR-13 3W8D TITLE CRYSTAL STRUCTURE OF D-3-HYDROXYBUTYRATE DEHYDROGENASE FROM TITLE 2 ALCALIGENES FAECALIS COMPLEXED WITH NAD+ AND AN INHIBITOR TITLE 3 METHYLMALONATE 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 METHYLMALONATE BINDING, KEYWDS 2 MITOCHONDRIA, OXIDOREDUCTASE, OXIDOREDUCTASE-OXIDOREDUCTASE KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.KANAZAWA,M.TSUNODA,M.M.HOQUE,K.SUZUKI,T.YAMAMOTO,A.TAKENAKA REVDAT 2 08-NOV-23 3W8D 1 REMARK LINK REVDAT 1 12-MAR-14 3W8D 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 METHYLMALONATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.37 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) : 1.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 49937 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 5084 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) : 1.37 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3228 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 359 REMARK 3 BIN FREE R VALUE : 0.2480 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 : 56 REMARK 3 SOLVENT ATOMS : 305 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.07 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): 0.056 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.059 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.033 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.790 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2030 ; 0.029 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2776 ; 2.447 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 275 ; 6.213 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 72 ;37.373 ;25.556 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 334 ;13.770 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;12.160 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 332 ; 0.166 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1493 ; 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): 1311 ; 1.271 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2095 ; 1.999 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 719 ; 3.279 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 673 ; 5.308 ; 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 3W8D 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_1000096014. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.4 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 : 50566 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.370 REMARK 200 RESOLUTION RANGE LOW (A) : 22.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 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) : 1.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 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 (%): 43.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 34% PEG 4000, 100MM TRIS REMARK 280 HYDROCHLORIDE, 200MM SODIUM METHYLMALONATE, 5MM NAD+, PH 4.4, REMARK 280 VAPOR DIFFUSION, HANGING DROP, 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 31.37000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.37000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.61000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.37000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.37000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 59.61000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.37000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.37000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 59.61000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.37000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.37000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 59.61000 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: 18130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -276.0 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 304 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 507 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 610 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 OG SER A 201 O ILE A 206 1.89 REMARK 500 O HOH A 505 O HOH A 705 1.96 REMARK 500 O HOH A 522 O HOH A 586 2.07 REMARK 500 OE1 GLU A 101 O HOH A 697 2.18 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 40 CG GLU A 40 CD 0.096 REMARK 500 GLU A 43 CD GLU A 43 OE2 0.070 REMARK 500 GLU A 218 CD GLU A 218 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 GLU A 23 OE1 - CD - OE2 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP A 30 CB - CG - OD2 ANGL. DEV. = -7.1 DEGREES REMARK 500 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 46 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 71 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ASP A 72 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 207 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 LEU A 215 CA - CB - CG ANGL. DEV. = 14.9 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 84 104.58 -161.58 REMARK 500 ALA A 141 -119.08 -89.85 REMARK 500 SER A 142 161.21 177.97 REMARK 500 ASP A 254 16.19 -146.08 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 306 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 4 O REMARK 620 2 ASP A 85 OD1 89.4 REMARK 620 3 HOH A 640 O 87.9 107.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 305 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 64 O REMARK 620 2 ALA A 112 O 87.5 REMARK 620 3 HOH A 447 O 62.5 130.6 REMARK 620 4 HOH A 454 O 140.4 95.2 133.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 304 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 260 OXT REMARK 620 2 HOH A 476 O 88.2 REMARK 620 3 HOH A 705 O 82.1 146.1 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 DXX A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3W8E RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH NAD+ AND MALONATE. REMARK 900 RELATED ID: 3W8F 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-HYDOROXYBUTYRATE. 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 3W8D 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 DXX A 302 8 HET CL A 303 1 HET NA A 304 1 HET NA A 305 1 HET NA A 306 1 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM DXX METHYLMALONIC ACID HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION FORMUL 2 NAD C21 H27 N7 O14 P2 FORMUL 3 DXX C4 H6 O4 FORMUL 4 CL CL 1- FORMUL 5 NA 3(NA 1+) FORMUL 8 HOH *305(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 O GLY A 4 NA NA A 306 1555 1555 3.18 LINK O LEU A 64 NA NA A 305 1555 1555 3.05 LINK OD1 ASP A 85 NA NA A 306 1555 1555 2.66 LINK O ALA A 112 NA NA A 305 1555 1555 2.82 LINK OXT ARG A 260 NA NA A 304 1555 1555 2.39 LINK NA NA A 304 O HOH A 476 1555 1555 2.41 LINK NA NA A 304 O HOH A 705 1555 1555 2.33 LINK NA NA A 305 O HOH A 447 1555 1555 2.05 LINK NA NA A 305 O HOH A 454 1555 1555 3.05 LINK NA NA A 306 O HOH A 640 1555 1555 2.17 SITE 1 AC1 33 GLY A 11 THR A 13 SER A 14 GLY A 15 SITE 2 AC1 33 ILE A 16 ASN A 34 PHE A 36 ALA A 62 SITE 3 AC1 33 ASP A 63 LEU A 64 ASN A 90 GLY A 92 SITE 4 AC1 33 LEU A 113 ILE A 140 ALA A 141 SER A 142 SITE 5 AC1 33 TYR A 155 LYS A 159 PRO A 185 GLY A 186 SITE 6 AC1 33 TRP A 187 VAL A 188 THR A 190 PRO A 191 SITE 7 AC1 33 LEU A 192 VAL A 193 DXX A 302 HOH A 412 SITE 8 AC1 33 HOH A 432 HOH A 534 HOH A 564 HOH A 570 SITE 9 AC1 33 HOH A 583 SITE 1 AC2 10 GLN A 94 SER A 142 HIS A 144 LYS A 152 SITE 2 AC2 10 TYR A 155 TRP A 187 LEU A 192 GLN A 196 SITE 3 AC2 10 TRP A 257 NAD A 301 SITE 1 AC3 3 SER A 149 VAL A 150 LYS A 219 SITE 1 AC4 4 VAL A 147 ARG A 260 HOH A 476 HOH A 705 SITE 1 AC5 7 LEU A 64 SER A 65 ALA A 112 SER A 116 SITE 2 AC5 7 ALA A 117 HOH A 447 HOH A 454 SITE 1 AC6 4 GLY A 4 LYS A 6 ASP A 85 HOH A 640 CRYST1 62.740 62.740 119.220 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 0.015939 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015939 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008388 0.00000