HEADER OXIDOREDUCTASE 29-NOV-11 3VL3 TITLE 3-ISOPROPYLMALATE DEHYDROGENASE FROM SHEWANELLA ONEIDENSIS MR-1 AT 340 TITLE 2 MPA 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 3-ISOPROPYLMALATE DEHYDROGENASE, IPMDH, HIGH-PRESSURE, DIAMOND-ANVIL KEYWDS 2 CELL, DAC, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.NAGAE,N.WATANABE REVDAT 5 08-NOV-23 3VL3 1 REMARK SEQADV LINK REVDAT 4 22-NOV-17 3VL3 1 REMARK REVDAT 3 13-JAN-16 3VL3 1 KEYWDS REVDAT 2 26-FEB-14 3VL3 1 JRNL REVDAT 1 29-FEB-12 3VL3 0 JRNL AUTH T.NAGAE,T.KAWAMURA,L.M.G.CHAVAS,K.NIWA,M.HASEGAWA,C.KATO, JRNL AUTH 2 N.WATANABE JRNL TITL HIGH-PRESSURE-INDUCED WATER PENETRATION INTO JRNL TITL 2 3-ISOPROPYLMALATE DEHYDROGENASE JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 68 300 2012 JRNL REFN ISSN 0907-4449 JRNL PMID 22349232 JRNL DOI 10.1107/S0907444912001862 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 33560 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) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1680 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2374 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 117 REMARK 3 BIN FREE R VALUE : 0.2910 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 : 275 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.11000 REMARK 3 B22 (A**2) : 0.28000 REMARK 3 B33 (A**2) : -0.33000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.06000 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): 0.119 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.201 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2874 ; 0.030 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3892 ; 2.401 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 381 ; 6.089 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 128 ;32.643 ;23.906 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 503 ;15.944 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;19.362 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 433 ; 0.195 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2196 ; 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): 1828 ; 1.642 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2922 ; 2.748 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1046 ; 4.219 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 961 ; 6.842 ; 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 3VL3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000095179. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 293 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 : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.700 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 : 33575 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 91.6 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.32800 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 (%): 51.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, CALCIUM 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 51.91200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.93850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.91200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.93850 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: 6770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 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 -67.11487 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -66.17054 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 O HOH A 732 O HOH A 758 2.15 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 137 CB GLU A 137 CG 0.150 REMARK 500 PHE A 214 CE1 PHE A 214 CZ 0.123 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 ASP A 49 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 136 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 164 CG - CD - NE ANGL. DEV. = 12.7 DEGREES REMARK 500 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 175 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 185 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 185 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 LEU A 219 CB - CG - CD1 ANGL. DEV. = -11.0 DEGREES REMARK 500 ARG A 322 NE - CZ - NH2 ANGL. DEV. = -3.7 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 GLU A 80 26.21 -79.24 REMARK 500 PRO A 84 -9.13 -50.18 REMARK 500 ARG A 184 -113.35 -118.60 REMARK 500 VAL A 196 -34.59 -131.80 REMARK 500 ARG A 234 56.78 -140.18 REMARK 500 ASP A 239 -77.67 -115.18 REMARK 500 GLN A 313 75.80 -118.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 249 OD1 REMARK 620 2 ASP A 253 OD2 111.6 REMARK 620 3 IPM A 401 O3 93.4 136.7 REMARK 620 4 IPM A 401 O1 90.6 144.0 65.1 REMARK 620 5 HOH A 503 O 79.4 76.6 74.0 137.2 REMARK 620 6 HOH A 585 O 173.5 74.6 82.7 83.1 104.3 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 CA 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: 3VKZ RELATED DB: PDB REMARK 900 RELATED ID: 3VL2 RELATED DB: PDB REMARK 900 RELATED ID: 3VL4 RELATED DB: PDB REMARK 900 RELATED ID: 3VL6 RELATED DB: PDB REMARK 900 RELATED ID: 3VL7 RELATED DB: PDB DBREF 3VL3 A 2 364 UNP Q8E9N3 LEU3_SHEON 2 364 SEQADV 3VL3 MET A -10 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VL3 ARG A -9 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VL3 GLY A -8 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VL3 SER A -7 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VL3 HIS A -6 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VL3 HIS A -5 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VL3 HIS A -4 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VL3 HIS A -3 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VL3 HIS A -2 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VL3 HIS A -1 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VL3 GLY A 0 UNP Q8E9N3 EXPRESSION TAG SEQADV 3VL3 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 CA A 402 1 HET CL A 403 1 HETNAM IPM 3-ISOPROPYLMALIC ACID HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION FORMUL 2 IPM C7 H12 O5 FORMUL 3 CA CA 2+ FORMUL 4 CL CL 1- FORMUL 5 HOH *275(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 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 GLY A 129 1 8 HELIX 8 8 GLU A 153 GLU A 157 5 5 HELIX 9 9 SER A 166 GLY A 183 1 18 HELIX 10 10 LEU A 197 ALA A 211 1 15 HELIX 11 11 VAL A 212 PHE A 214 5 3 HELIX 12 12 ILE A 224 ARG A 234 1 11 HELIX 13 13 PRO A 235 PHE A 238 5 4 HELIX 14 14 SER A 244 GLY A 260 1 17 HELIX 15 15 SER A 261 LEU A 264 5 4 HELIX 16 16 ALA A 285 ALA A 289 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 SER A 339 ALA A 346 5 8 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 ALA A 6 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 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 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 CA CA A 402 1555 1555 2.28 LINK OD2 ASP A 253 CA CA A 402 1555 1555 2.40 LINK O3 IPM A 401 CA CA A 402 1555 1555 2.39 LINK O1 IPM A 401 CA CA A 402 1555 1555 2.59 LINK CA CA A 402 O HOH A 503 1555 1555 2.37 LINK CA CA A 402 O HOH A 585 1555 1555 2.41 CISPEP 1 LYS A 146 PRO A 147 0 1.94 SITE 1 AC1 11 GLU A 89 ARG A 97 ARG A 136 TYR A 143 SITE 2 AC1 11 LYS A 193 ASP A 225 ASP A 249 CA A 402 SITE 3 AC1 11 HOH A 503 HOH A 650 HOH A 693 SITE 1 AC2 6 ASP A 225 ASP A 249 ASP A 253 IPM A 401 SITE 2 AC2 6 HOH A 503 HOH A 585 SITE 1 AC3 5 GLY A 141 ILE A 142 ASN A 245 LEU A 246 SITE 2 AC3 5 HOH A 600 CRYST1 103.824 57.877 75.671 90.00 119.02 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 0.009632 0.000000 0.005343 0.00000 SCALE2 0.000000 0.017278 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015112 0.00000