HEADER OXIDOREDUCTASE 13-DEC-11 3VMJ TITLE 3-ISOPROPYLMALATE DEHYDROGENASE FROM SHEWANELLA ONEIDENSIS MR-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-ISOPROPYLMALATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 3-IPM-DH, BETA-IPM DEHYDROGENASE, IMDH; COMPND 5 EC: 1.1.1.85; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHEWANELLA ONEIDENSIS; SOURCE 3 ORGANISM_TAXID: 211586; SOURCE 4 STRAIN: MR-1; SOURCE 5 GENE: LEUB, SO_4235; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 CODONPLUS(DE3) RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE80 KEYWDS OXIDOREDUCTASE, DECARBOXYLATING DEHYDROGENASE EXPDTA X-RAY DIFFRACTION AUTHOR T.NAGAE,N.WATANABE REVDAT 4 08-NOV-23 3VMJ 1 REMARK SEQADV LINK REVDAT 3 22-NOV-17 3VMJ 1 REMARK REVDAT 2 12-JUN-13 3VMJ 1 JRNL REVDAT 1 29-FEB-12 3VMJ 0 JRNL AUTH T.NAGAE,C.KATO,N.WATANABE JRNL TITL STRUCTURAL ANALYSIS OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM JRNL TITL 2 THE OBLIGATE PIEZOPHILE SHEWANELLA BENTHICA DB21MT-2 AND THE JRNL TITL 3 NONPIEZOPHILE SHEWANELLA ONEIDENSIS MR-1 JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 68 265 2012 JRNL REFN ESSN 1744-3091 JRNL PMID 22442218 JRNL DOI 10.1107/S1744309112001443 REMARK 2 REMARK 2 RESOLUTION. 1.56 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) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 52465 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2807 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) : 1.56 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.60 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3509 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE SET COUNT : 218 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2759 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 368 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.83000 REMARK 3 B22 (A**2) : -0.65000 REMARK 3 B33 (A**2) : -0.40000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.80000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.080 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.085 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.617 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2899 ; 0.030 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3935 ; 2.500 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 391 ; 5.859 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 127 ;31.552 ;23.701 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 510 ;14.753 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;17.631 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 440 ; 0.163 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2217 ; 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): 1846 ; 1.522 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2958 ; 2.411 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1053 ; 3.732 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 962 ; 5.771 ; 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 3VMJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000095231. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55280 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.25500 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: PDB ENTRY 3VKZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, SODIUM CHLORIDE, HEPES, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 51.34150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.74750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.34150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.74750 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: 6590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 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 -65.64253 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -66.74034 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 868 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -10 REMARK 465 ARG A -9 REMARK 465 GLY A -8 REMARK 465 SER A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 GLY A 0 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 OE1 GLU A 179 O HOH A 783 2.08 REMARK 500 OG SER A 267 O HOH A 839 2.10 REMARK 500 O HOH A 864 O HOH A 865 2.10 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 ARG A 164 CG ARG A 164 CD 0.160 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 22 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 22 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP A 42 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 107 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 128 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP A 161 OD1 - CG - OD2 ANGL. DEV. = 12.3 DEGREES REMARK 500 ASP A 161 CB - CG - OD1 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP A 161 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 164 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 TYR A 165 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 TYR A 165 CD1 - CE1 - CZ ANGL. DEV. = -6.7 DEGREES REMARK 500 ASP A 192 CB - CG - OD2 ANGL. DEV. = -8.6 DEGREES REMARK 500 ASP A 225 CB - CG - OD2 ANGL. DEV. = -11.8 DEGREES REMARK 500 ASP A 249 CB - CG - OD1 ANGL. DEV. = -6.6 DEGREES REMARK 500 ASP A 253 CB - CG - OD1 ANGL. DEV. = -9.6 DEGREES REMARK 500 MET A 270 CG - SD - CE ANGL. DEV. = -28.8 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 8 78.78 -118.00 REMARK 500 HIS A 51 -8.18 -141.10 REMARK 500 ARG A 184 -120.72 -124.80 REMARK 500 VAL A 196 -41.01 -133.18 REMARK 500 ARG A 234 52.83 -148.50 REMARK 500 ASP A 239 -73.95 -119.06 REMARK 500 SER A 244 -178.40 -68.75 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 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 249 OD1 REMARK 620 2 IPM A 401 O1 98.9 REMARK 620 3 IPM A 401 O3 88.4 75.0 REMARK 620 4 HOH A 832 O 170.6 86.1 85.2 REMARK 620 5 HOH A 834 O 88.2 164.3 91.4 85.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPM A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VMK RELATED DB: PDB REMARK 900 RELATED ID: 3VML RELATED DB: PDB DBREF 3VMJ A 2 364 UNP Q8E9N3 LEU3_SHEON 2 364 SEQADV 3VMJ MET A -10 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VMJ ARG A -9 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VMJ GLY A -8 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VMJ SER A -7 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VMJ HIS A -6 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VMJ HIS A -5 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VMJ HIS A -4 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VMJ HIS A -3 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VMJ HIS A -2 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VMJ HIS A -1 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VMJ GLY A 0 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VMJ SER A 1 UNP Q8E9N3 EXPRESSION TAG SEQRES 1 A 375 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER SER SEQRES 2 A 375 TYR GLN ILE ALA VAL LEU ALA GLY ASP GLY ILE GLY PRO SEQRES 3 A 375 GLU VAL MET ALA GLU ALA ARG LYS VAL LEU LYS ALA VAL SEQRES 4 A 375 GLU ALA ARG PHE GLY LEU ASN ILE GLU TYR THR GLU TYR SEQRES 5 A 375 ASP VAL GLY GLY ILE ALA ILE ASP ASN HIS GLY CYS PRO SEQRES 6 A 375 LEU PRO GLU ALA THR LEU LYS GLY CYS GLU ALA ALA ASP SEQRES 7 A 375 ALA ILE LEU PHE GLY SER VAL GLY GLY PRO LYS TRP GLU SEQRES 8 A 375 LYS LEU PRO PRO ASN GLU GLN PRO GLU ARG GLY ALA LEU SEQRES 9 A 375 LEU PRO LEU ARG GLY HIS PHE GLU LEU PHE CYS ASN LEU SEQRES 10 A 375 ARG PRO ALA LYS LEU HIS ASP GLY LEU GLU HIS MET SER SEQRES 11 A 375 PRO LEU ARG SER ASP ILE SER ALA ARG GLY PHE ASP VAL SEQRES 12 A 375 LEU CYS VAL ARG GLU LEU THR GLY GLY ILE TYR PHE GLY SEQRES 13 A 375 LYS PRO LYS GLY ARG GLN GLY GLU GLY GLU SER GLU GLU SEQRES 14 A 375 ALA PHE ASP THR MET ARG TYR SER ARG ARG GLU ILE SER SEQRES 15 A 375 ARG ILE ALA ARG ILE ALA PHE GLU ALA ALA ARG GLY ARG SEQRES 16 A 375 ARG LYS LYS VAL THR SER VAL ASP LYS ALA ASN VAL LEU SEQRES 17 A 375 ALA CYS SER VAL LEU TRP ARG GLN VAL VAL GLU GLU VAL SEQRES 18 A 375 ALA VAL ASP PHE PRO ASP VAL GLU LEU GLU HIS ILE TYR SEQRES 19 A 375 ILE ASP ASN ALA THR MET GLN LEU LEU ARG ARG PRO ASP SEQRES 20 A 375 GLU PHE ASP VAL MET LEU CYS SER ASN LEU PHE GLY ASP SEQRES 21 A 375 ILE LEU SER ASP GLU ILE ALA MET LEU THR GLY SER MET SEQRES 22 A 375 GLY LEU LEU SER SER ALA SER MET ASN SER THR GLY PHE SEQRES 23 A 375 GLY LEU PHE GLU PRO ALA GLY GLY SER ALA PRO ASP ILE SEQRES 24 A 375 ALA GLY LYS GLY ILE ALA ASN PRO ILE ALA GLN ILE LEU SEQRES 25 A 375 SER ALA ALA LEU MET LEU ARG HIS SER LEU LYS GLN GLU SEQRES 26 A 375 GLU ALA ALA SER ALA ILE GLU ARG ALA VAL THR LYS ALA SEQRES 27 A 375 LEU ASN SER GLY TYR LEU THR GLY GLU LEU LEU SER SER SEQRES 28 A 375 ASP GLN ARG HIS LYS ALA LYS THR THR VAL GLN MET GLY SEQRES 29 A 375 ASP PHE ILE ALA ASP ALA VAL LYS ALA GLY VAL HET IPM A 401 12 HET MG A 402 1 HET CL A 403 1 HETNAM IPM 3-ISOPROPYLMALIC ACID HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION FORMUL 2 IPM C7 H12 O5 FORMUL 3 MG MG 2+ FORMUL 4 CL CL 1- FORMUL 5 HOH *368(H2 O) HELIX 1 1 ILE A 13 GLY A 33 1 21 HELIX 2 2 GLY A 44 GLY A 52 1 9 HELIX 3 3 PRO A 56 ALA A 65 1 10 HELIX 4 4 GLY A 76 GLU A 80 5 5 HELIX 5 5 PRO A 83 GLU A 86 5 4 HELIX 6 6 GLN A 87 PHE A 100 1 14 HELIX 7 7 LEU A 115 SER A 119 5 5 HELIX 8 8 ARG A 122 ALA A 127 1 6 HELIX 9 9 GLU A 153 GLU A 157 5 5 HELIX 10 10 SER A 166 GLY A 183 1 18 HELIX 11 11 LEU A 197 ALA A 211 1 15 HELIX 12 12 VAL A 212 PHE A 214 5 3 HELIX 13 13 ILE A 224 ARG A 234 1 11 HELIX 14 14 PRO A 235 PHE A 238 5 4 HELIX 15 15 SER A 244 THR A 259 1 16 HELIX 16 16 GLY A 260 LEU A 264 5 5 HELIX 17 17 PRO A 296 SER A 310 1 15 HELIX 18 18 GLN A 313 SER A 330 1 18 HELIX 19 19 THR A 334 LEU A 338 5 5 HELIX 20 20 ASP A 341 ALA A 346 5 6 HELIX 21 21 THR A 348 ALA A 362 1 15 SHEET 1 A10 ILE A 36 GLU A 40 0 SHEET 2 A10 TYR A 3 GLY A 10 1 N VAL A 7 O THR A 39 SHEET 3 A10 ALA A 68 SER A 73 1 O LEU A 70 N LEU A 8 SHEET 4 A10 GLY A 276 PRO A 280 1 O PHE A 278 N PHE A 71 SHEET 5 A10 SER A 266 MET A 270 -1 N SER A 269 O LEU A 277 SHEET 6 A10 CYS A 104 LYS A 110 -1 N LEU A 106 O ALA A 268 SHEET 7 A10 ASP A 131 GLU A 137 -1 O VAL A 132 N ALA A 109 SHEET 8 A10 VAL A 240 CYS A 243 1 O CYS A 243 N VAL A 135 SHEET 9 A10 LYS A 187 ASP A 192 1 N THR A 189 O VAL A 240 SHEET 10 A10 GLU A 218 TYR A 223 1 O GLU A 220 N SER A 190 SHEET 1 B 2 GLY A 149 GLN A 151 0 SHEET 2 B 2 GLU A 158 PHE A 160 -1 O GLU A 158 N GLN A 151 LINK OD1 ASP A 249 MG MG A 402 1555 1555 2.04 LINK O1 IPM A 401 MG MG A 402 1555 1555 2.17 LINK O3 IPM A 401 MG MG A 402 1555 1555 2.22 LINK MG MG A 402 O HOH A 832 1555 1555 2.09 LINK MG MG A 402 O HOH A 834 1555 1555 2.06 CISPEP 1 LYS A 146 PRO A 147 0 4.73 SITE 1 AC1 13 ARG A 97 ARG A 136 TYR A 143 LYS A 193 SITE 2 AC1 13 ASN A 195 ASP A 225 ASP A 249 MG A 402 SITE 3 AC1 13 HOH A 597 HOH A 772 HOH A 832 HOH A 834 SITE 4 AC1 13 HOH A 859 SITE 1 AC2 5 ASP A 225 ASP A 249 IPM A 401 HOH A 832 SITE 2 AC2 5 HOH A 834 SITE 1 AC3 5 GLY A 141 ILE A 142 ASN A 245 LEU A 246 SITE 2 AC3 5 HOH A 562 CRYST1 102.683 57.495 76.330 90.00 119.03 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 0.009739 0.000000 0.005405 0.00000 SCALE2 0.000000 0.017393 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014983 0.00000