HEADER OXIDOREDUCTASE 13-DEC-11 3VMK TITLE 3-ISOPROPYLMALATE DEHYDROGENASE FROM SHEWANELLA BENTHICA DB21 MT-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-ISOPROPYLMALATE DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.1.1.85; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHEWANELLA BENTHICA; SOURCE 3 ORGANISM_TAXID: 43661; SOURCE 4 STRAIN: DB21 MT-2; SOURCE 5 GENE: LEUB; 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 3VMK 1 REMARK SEQADV LINK REVDAT 3 22-NOV-17 3VMK 1 REMARK REVDAT 2 12-JUN-13 3VMK 1 JRNL REVDAT 1 29-FEB-12 3VMK 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. 1.48 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) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 118063 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5928 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) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8004 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE SET COUNT : 426 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5594 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 709 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.76000 REMARK 3 B22 (A**2) : 1.01000 REMARK 3 B33 (A**2) : -0.31000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.36000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.054 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.418 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5798 ; 0.029 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7854 ; 2.446 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 764 ; 6.147 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 254 ;33.137 ;24.291 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 999 ;13.011 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;19.010 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 864 ; 0.177 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4430 ; 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): 3696 ; 1.534 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5900 ; 2.261 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2102 ; 3.326 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1939 ; 5.013 ; 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3VMK 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_1000095232. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A 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 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 118167 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 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 (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.32200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 45.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, SODIUM CHLORIDE, HEPES, PH REMARK 280 6.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 29.60400 REMARK 290 SMTRY3 2 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: 6430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 VAL A 364 REMARK 465 MET B -10 REMARK 465 ARG B -9 REMARK 465 GLY B -8 REMARK 465 SER B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 VAL B 364 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 244 O HOH A 747 1.94 REMARK 500 OE1 GLN B 151 OE1 GLU B 158 2.12 REMARK 500 O HIS B -1 N SER B 1 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 TYR A 38 CE1 TYR A 38 CZ 0.123 REMARK 500 VAL A 207 CB VAL A 207 CG2 0.139 REMARK 500 TYR A 223 CD1 TYR A 223 CE1 0.111 REMARK 500 SER A 261 CB SER A 261 OG 0.102 REMARK 500 GLY B 0 N GLY B 0 CA 0.099 REMARK 500 GLY B 154 N GLY B 154 CA 0.120 REMARK 500 TYR B 223 CZ TYR B 223 CE2 -0.086 REMARK 500 CYS B 335 CA CYS B 335 CB 0.140 REMARK 500 CYS B 335 CB CYS B 335 SG 0.117 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. = -4.2 DEGREES REMARK 500 ARG A 22 NE - CZ - NH2 ANGL. DEV. = 4.6 DEGREES REMARK 500 ASP A 42 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 42 CB - CG - OD2 ANGL. DEV. = -8.1 DEGREES REMARK 500 ARG A 164 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 167 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 184 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 185 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 185 NE - CZ - NH2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 204 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 233 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 234 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ASP A 249 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 253 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 308 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 308 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 LEU A 318 CB - CG - CD1 ANGL. DEV. = 12.3 DEGREES REMARK 500 ASP A 354 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 GLY B 0 N - CA - C ANGL. DEV. = 15.8 DEGREES REMARK 500 ASP B 42 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 49 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG B 136 NH1 - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG B 136 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 136 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 TYR B 143 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG B 184 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 PHE B 275 CB - CG - CD1 ANGL. DEV. = 4.4 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 PRO A 83 178.84 -56.27 REMARK 500 ARG A 184 -113.29 -117.91 REMARK 500 ARG A 234 51.44 -147.03 REMARK 500 ASP A 239 -77.92 -122.27 REMARK 500 ALA A 285 58.58 39.68 REMARK 500 LEU A 313 75.52 -100.72 REMARK 500 ARG B 184 -107.37 -121.69 REMARK 500 VAL B 196 -42.65 -139.60 REMARK 500 ARG B 234 51.99 -146.48 REMARK 500 ASP B 239 -76.53 -118.03 REMARK 500 SER B 244 -179.85 -65.75 REMARK 500 ALA B 285 60.46 33.54 REMARK 500 LEU B 313 79.81 -103.33 REMARK 500 CYS B 335 -57.58 -29.78 REMARK 500 ALA B 361 59.09 -63.87 REMARK 500 GLU B 362 17.33 -164.32 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 B 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 225 OD1 REMARK 620 2 HOH A 551 O 90.0 REMARK 620 3 ASP B 249 OD1 93.2 172.1 REMARK 620 4 IPM B 401 O1 90.9 88.0 99.3 REMARK 620 5 IPM B 401 O3 167.6 87.7 90.7 76.9 REMARK 620 6 HOH B 506 O 98.6 83.9 88.4 167.5 93.3 REMARK 620 N 1 2 3 4 5 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 O3 87.7 REMARK 620 3 IPM A 401 O1 98.0 71.3 REMARK 620 4 HOH A 682 O 89.3 101.1 169.1 REMARK 620 5 ASP B 225 OD1 94.6 155.7 84.4 103.2 REMARK 620 6 HOH B 741 O 177.2 93.0 84.8 87.9 85.9 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 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 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPM B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VMJ RELATED DB: PDB REMARK 900 RELATED ID: 3VML RELATED DB: PDB DBREF 3VMK A 2 364 UNP D2YZL2 D2YZL2_9GAMM 2 364 DBREF 3VMK B 2 364 UNP D2YZL2 D2YZL2_9GAMM 2 364 SEQADV 3VMK MET A -10 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK ARG A -9 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK GLY A -8 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK SER A -7 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK HIS A -6 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK HIS A -5 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK HIS A -4 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK HIS A -3 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK HIS A -2 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK HIS A -1 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK GLY A 0 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK SER A 1 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK MET B -10 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK ARG B -9 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK GLY B -8 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK SER B -7 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK HIS B -6 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK HIS B -5 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK HIS B -4 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK HIS B -3 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK HIS B -2 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK HIS B -1 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK GLY B 0 UNP D2YZL2 EXPRESSION TAG SEQADV 3VMK SER B 1 UNP D2YZL2 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 ALA ALA VAL SEQRES 4 A 375 GLU LYS ARG PHE ASP LEU SER ILE GLU TYR SER GLU TYR SEQRES 5 A 375 ASP VAL GLY GLY ALA 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 VAL LEU PHE GLY SER VAL GLY GLY PRO LYS TRP GLU SEQRES 8 A 375 HIS LEU PRO PRO ASN ASP GLN PRO GLU ARG GLY ALA LEU SEQRES 9 A 375 LEU PRO LEU ARG GLY HIS PHE GLU LEU PHE CYS ASN MET SEQRES 10 A 375 ARG PRO ALA LYS LEU HIS PRO GLY LEU GLU HIS MET SER SEQRES 11 A 375 PRO LEU ARG SER ASP ILE SER GLU LYS GLY PHE ASP ILE 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 ASN GLU GLU SEQRES 14 A 375 ALA PHE ASP THR MET ARG TYR SER ARG LYS GLU ILE ARG SEQRES 15 A 375 ARG ILE ALA LYS ILE ALA PHE GLU SER ALA GLN 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 GLU VAL VAL GLU GLU VAL SEQRES 18 A 375 ALA LYS ASP TYR 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 ASN SEQRES 20 A 375 GLU PHE ASP VAL MET LEU CYS SER ASN LEU PHE GLY ASP SEQRES 21 A 375 ILE VAL SER ASP GLU ILE ALA MET LEU THR GLY SER MET SEQRES 22 A 375 GLY LEU LEU ALA SER ILE SER MET ASN SER GLN GLY PHE SEQRES 23 A 375 GLY MET TYR GLU PRO ALA GLY GLY SER ALA PRO ASP ILE SEQRES 24 A 375 ALA GLY GLN GLY ILE ALA ASN PRO VAL ALA GLN ILE LEU SEQRES 25 A 375 SER ALA ALA LEU LEU LEU ARG HIS SER LEU LYS LEU GLU SEQRES 26 A 375 ASP ALA ALA LEU ALA ILE GLU ALA ALA VAL SER LYS ALA SEQRES 27 A 375 LEU SER ASP GLY TYR LEU THR CYS GLU LEU LEU PRO ALA SEQRES 28 A 375 SER GLU ARG SER GLN ALA LYS SER THR SER GLN MET GLY SEQRES 29 A 375 ASP TYR ILE ALA GLN ALA ILE ALA GLU GLY VAL SEQRES 1 B 375 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER SER SEQRES 2 B 375 TYR GLN ILE ALA VAL LEU ALA GLY ASP GLY ILE GLY PRO SEQRES 3 B 375 GLU VAL MET ALA GLU ALA ARG LYS VAL LEU ALA ALA VAL SEQRES 4 B 375 GLU LYS ARG PHE ASP LEU SER ILE GLU TYR SER GLU TYR SEQRES 5 B 375 ASP VAL GLY GLY ALA ALA ILE ASP ASN HIS GLY CYS PRO SEQRES 6 B 375 LEU PRO GLU ALA THR LEU LYS GLY CYS GLU ALA ALA ASP SEQRES 7 B 375 ALA VAL LEU PHE GLY SER VAL GLY GLY PRO LYS TRP GLU SEQRES 8 B 375 HIS LEU PRO PRO ASN ASP GLN PRO GLU ARG GLY ALA LEU SEQRES 9 B 375 LEU PRO LEU ARG GLY HIS PHE GLU LEU PHE CYS ASN MET SEQRES 10 B 375 ARG PRO ALA LYS LEU HIS PRO GLY LEU GLU HIS MET SER SEQRES 11 B 375 PRO LEU ARG SER ASP ILE SER GLU LYS GLY PHE ASP ILE SEQRES 12 B 375 LEU CYS VAL ARG GLU LEU THR GLY GLY ILE TYR PHE GLY SEQRES 13 B 375 LYS PRO LYS GLY ARG GLN GLY GLU GLY GLU ASN GLU GLU SEQRES 14 B 375 ALA PHE ASP THR MET ARG TYR SER ARG LYS GLU ILE ARG SEQRES 15 B 375 ARG ILE ALA LYS ILE ALA PHE GLU SER ALA GLN GLY ARG SEQRES 16 B 375 ARG LYS LYS VAL THR SER VAL ASP LYS ALA ASN VAL LEU SEQRES 17 B 375 ALA CYS SER VAL LEU TRP ARG GLU VAL VAL GLU GLU VAL SEQRES 18 B 375 ALA LYS ASP TYR PRO ASP VAL GLU LEU GLU HIS ILE TYR SEQRES 19 B 375 ILE ASP ASN ALA THR MET GLN LEU LEU ARG ARG PRO ASN SEQRES 20 B 375 GLU PHE ASP VAL MET LEU CYS SER ASN LEU PHE GLY ASP SEQRES 21 B 375 ILE VAL SER ASP GLU ILE ALA MET LEU THR GLY SER MET SEQRES 22 B 375 GLY LEU LEU ALA SER ILE SER MET ASN SER GLN GLY PHE SEQRES 23 B 375 GLY MET TYR GLU PRO ALA GLY GLY SER ALA PRO ASP ILE SEQRES 24 B 375 ALA GLY GLN GLY ILE ALA ASN PRO VAL ALA GLN ILE LEU SEQRES 25 B 375 SER ALA ALA LEU LEU LEU ARG HIS SER LEU LYS LEU GLU SEQRES 26 B 375 ASP ALA ALA LEU ALA ILE GLU ALA ALA VAL SER LYS ALA SEQRES 27 B 375 LEU SER ASP GLY TYR LEU THR CYS GLU LEU LEU PRO ALA SEQRES 28 B 375 SER GLU ARG SER GLN ALA LYS SER THR SER GLN MET GLY SEQRES 29 B 375 ASP TYR ILE ALA GLN ALA ILE ALA GLU GLY VAL HET IPM A 401 12 HET MG A 402 1 HET CL A 403 1 HET IPM B 401 12 HET MG B 402 1 HET CL B 403 1 HETNAM IPM 3-ISOPROPYLMALIC ACID HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION FORMUL 3 IPM 2(C7 H12 O5) FORMUL 4 MG 2(MG 2+) FORMUL 5 CL 2(CL 1-) FORMUL 9 HOH *709(H2 O) HELIX 1 1 ILE A 13 PHE A 32 1 20 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 GLN A 87 PHE A 100 1 14 HELIX 6 6 LEU A 115 SER A 119 5 5 HELIX 7 7 ARG A 122 GLU A 127 1 6 HELIX 8 8 GLU A 153 ASN A 156 5 4 HELIX 9 9 ARG A 167 GLY A 183 1 17 HELIX 10 10 LEU A 197 LYS A 212 1 16 HELIX 11 11 ILE A 224 ARG A 234 1 11 HELIX 12 12 PRO A 235 PHE A 238 5 4 HELIX 13 13 SER A 244 GLY A 260 1 17 HELIX 14 14 SER A 261 LEU A 264 5 4 HELIX 15 15 PRO A 296 SER A 310 1 15 HELIX 16 16 LEU A 313 ASP A 330 1 18 HELIX 17 17 THR A 334 LEU A 338 5 5 HELIX 18 18 PRO A 339 ALA A 346 5 8 HELIX 19 19 SER A 348 GLU A 362 1 15 HELIX 20 20 ILE B 13 ASP B 33 1 21 HELIX 21 21 GLY B 44 GLY B 52 1 9 HELIX 22 22 PRO B 56 ALA B 65 1 10 HELIX 23 23 GLY B 76 GLU B 80 5 5 HELIX 24 24 PRO B 83 ASP B 86 5 4 HELIX 25 25 GLN B 87 PHE B 100 1 14 HELIX 26 26 LEU B 115 SER B 119 5 5 HELIX 27 27 ARG B 122 GLU B 127 1 6 HELIX 28 28 GLU B 153 ASN B 156 5 4 HELIX 29 29 ARG B 167 GLY B 183 1 17 HELIX 30 30 LEU B 197 ASP B 213 1 17 HELIX 31 31 ILE B 224 ARG B 234 1 11 HELIX 32 32 PRO B 235 PHE B 238 5 4 HELIX 33 33 SER B 244 GLY B 260 1 17 HELIX 34 34 SER B 261 LEU B 264 5 4 HELIX 35 35 PRO B 296 SER B 310 1 15 HELIX 36 36 LEU B 313 ASP B 330 1 18 HELIX 37 37 THR B 334 LEU B 338 5 5 HELIX 38 38 PRO B 339 ALA B 346 5 8 HELIX 39 39 SER B 348 ALA B 361 1 14 SHEET 1 A10 ILE A 36 GLU A 40 0 SHEET 2 A10 TYR A 3 GLY A 10 1 N TYR A 3 O GLU A 37 SHEET 3 A10 ALA A 68 SER A 73 1 O GLY A 72 N LEU A 8 SHEET 4 A10 GLY A 276 PRO A 280 1 O TYR A 278 N PHE A 71 SHEET 5 A10 ALA A 266 MET A 270 -1 N SER A 267 O GLU A 279 SHEET 6 A10 CYS A 104 LYS A 110 -1 N MET A 106 O ILE A 268 SHEET 7 A10 ASP A 131 GLU A 137 -1 O ILE A 132 N ALA A 109 SHEET 8 A10 VAL A 240 CYS A 243 1 O MET A 241 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 218 N VAL A 188 SHEET 1 B 4 GLY A 149 GLN A 151 0 SHEET 2 B 4 GLU A 158 SER A 166 -1 O GLU A 158 N GLN A 151 SHEET 3 B 4 GLU B 158 SER B 166 -1 O TYR B 165 N ALA A 159 SHEET 4 B 4 GLY B 149 GLN B 151 -1 N GLN B 151 O GLU B 158 SHEET 1 C10 ILE B 36 GLU B 40 0 SHEET 2 C10 TYR B 3 GLY B 10 1 N VAL B 7 O SER B 39 SHEET 3 C10 ALA B 68 SER B 73 1 O GLY B 72 N LEU B 8 SHEET 4 C10 GLY B 276 PRO B 280 1 O TYR B 278 N PHE B 71 SHEET 5 C10 ALA B 266 MET B 270 -1 N SER B 269 O MET B 277 SHEET 6 C10 CYS B 104 LYS B 110 -1 N CYS B 104 O MET B 270 SHEET 7 C10 ASP B 131 GLU B 137 -1 O ARG B 136 N ASN B 105 SHEET 8 C10 VAL B 240 CYS B 243 1 O MET B 241 N VAL B 135 SHEET 9 C10 LYS B 187 ASP B 192 1 N THR B 189 O VAL B 240 SHEET 10 C10 GLU B 218 TYR B 223 1 O GLU B 218 N VAL B 188 LINK OD1 ASP A 225 MG MG B 402 1555 1555 2.03 LINK OD1 ASP A 249 MG MG A 402 1555 1555 1.99 LINK O3 IPM A 401 MG MG A 402 1555 1555 2.09 LINK O1 IPM A 401 MG MG A 402 1555 1555 2.25 LINK MG MG A 402 O HOH A 682 1555 1555 1.96 LINK MG MG A 402 OD1 ASP B 225 1555 1555 2.08 LINK MG MG A 402 O HOH B 741 1555 1555 2.06 LINK O HOH A 551 MG MG B 402 1555 1555 2.06 LINK OD1 ASP B 249 MG MG B 402 1555 1555 2.06 LINK O1 IPM B 401 MG MG B 402 1555 1555 2.11 LINK O3 IPM B 401 MG MG B 402 1555 1555 2.12 LINK MG MG B 402 O HOH B 506 1555 1555 2.06 CISPEP 1 LYS A 146 PRO A 147 0 1.46 CISPEP 2 LYS B 146 PRO B 147 0 5.90 SITE 1 AC1 12 ARG A 97 ARG A 136 TYR A 143 ASP A 249 SITE 2 AC1 12 MG A 402 HOH A 559 HOH A 634 HOH A 771 SITE 3 AC1 12 LYS B 193 ASN B 195 ASP B 225 HOH B 741 SITE 1 AC2 5 ASP A 249 IPM A 401 HOH A 682 ASP B 225 SITE 2 AC2 5 HOH B 741 SITE 1 AC3 4 GLY A 141 ILE A 142 LEU A 246 HOH A 747 SITE 1 AC4 14 LYS A 193 ASN A 195 ASP A 225 HOH A 551 SITE 2 AC4 14 ARG B 97 ARG B 107 ARG B 136 TYR B 143 SITE 3 AC4 14 ASP B 249 MG B 402 HOH B 506 HOH B 618 SITE 4 AC4 14 HOH B 647 HOH B 795 SITE 1 AC5 5 ASP A 225 HOH A 551 ASP B 249 IPM B 401 SITE 2 AC5 5 HOH B 506 SITE 1 AC6 5 GLY B 141 ILE B 142 ASN B 245 LEU B 246 SITE 2 AC6 5 HOH B 803 CRYST1 51.972 59.208 119.779 90.00 95.12 90.00 P 1 21 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 0.019241 0.000000 0.001724 0.00000 SCALE2 0.000000 0.016890 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008382 0.00000