HEADER OXIDOREDUCTASE 04-JAN-11 2Y3Z TITLE STRUCTURE OF ISOPROPYLMALATE DEHYDROGENASE FROM THERMUS THERMOPHILUS - TITLE 2 APO ENZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-ISOPROPYLMALATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ISOPROPYLMALATE DEHYDROGENASE, 3-IPM-DH, BETA-IPM COMPND 5 DEHYDROGENASE, IMDH, IPMDH; COMPND 6 EC: 1.1.1.85; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: ADDITIONAL AMINO ACIDS- N-TERMINAL MAS. C- TERMINAL COMPND 9 AAALEHHHHHH SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET21C KEYWDS OXIDOREDUCTASE, LEUB, LEUCINE BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR E.GRACZER,A.MERLIN,R.K.SINGH,K.MANIKANDAN,P.ZAVODSKY,M.S.WEISS,M.VAS REVDAT 3 20-DEC-23 2Y3Z 1 REMARK REVDAT 2 18-APR-12 2Y3Z 1 JRNL REVDAT 1 19-JAN-11 2Y3Z 0 JRNL AUTH E.GRACZER,A.MERLI,R.K.SINGH,M.KARUPPASAMY,P.ZAVODSZKY, JRNL AUTH 2 M.S.WEISS,M.VAS JRNL TITL ATOMIC LEVEL DESCRIPTION OF THE DOMAIN CLOSURE IN A DIMERIC JRNL TITL 2 ENZYME: THERMUS THERMOPHILUS 3-ISOPROPYLMALATE JRNL TITL 3 DEHYDROGENASE. JRNL REF MOL.BIOSYST. V. 7 1646 2011 JRNL REFN ISSN 1742-206X JRNL PMID 21387033 JRNL DOI 10.1039/C0MB00346H REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.MERLI,K.MANIKANDAN,E.GRACZER,L.SCHULDT,R.K.SINGH, REMARK 1 AUTH 2 P.ZAVODSZKY,M.VAS,M.S.WEISS REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION ANALYSIS REMARK 1 TITL 2 OF VARIOUS ENZYME-SUBSTRATE COMPLEXES OF ISOPROPYLMALATE REMARK 1 TITL 3 DEHYDROGENASE FROM THERMUS THERMOPHILUS. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 66 738 2010 REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 20516614 REMARK 1 DOI 10.1107/S174430911001626X REMARK 2 REMARK 2 RESOLUTION. 1.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 45360 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1193 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) : 1.83 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3167 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2632 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 82 REMARK 3 SOLVENT ATOMS : 201 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : -0.06000 REMARK 3 B33 (A**2) : 0.08000 REMARK 3 B12 (A**2) : -0.03000 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): 0.090 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.093 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.530 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2809 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3787 ; 1.852 ; 2.010 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 350 ; 5.699 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 114 ;33.286 ;22.982 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 455 ;12.401 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;23.112 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 424 ; 0.149 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2074 ; 0.010 ; 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): 1757 ; 1.183 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2822 ; 2.034 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1052 ; 4.886 ; 5.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 965 ; 7.714 ;10.000 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 350 REMARK 3 ORIGIN FOR THE GROUP (A): 18.5827 34.5974 18.3754 REMARK 3 T TENSOR REMARK 3 T11: 0.0041 T22: 0.0884 REMARK 3 T33: 0.0534 T12: 0.0023 REMARK 3 T13: 0.0102 T23: -0.0370 REMARK 3 L TENSOR REMARK 3 L11: 1.2871 L22: 0.4989 REMARK 3 L33: 1.5702 L12: 0.2503 REMARK 3 L13: 0.6235 L23: 0.0374 REMARK 3 S TENSOR REMARK 3 S11: 0.0128 S12: -0.0822 S13: 0.0088 REMARK 3 S21: -0.0091 S22: -0.0245 S23: -0.0450 REMARK 3 S31: -0.0111 S32: -0.0450 S33: 0.0117 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 2Y3Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1290046886. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9334 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47324 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.65000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 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 1HEX REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PEG-550-MME, 0.1 M TRIS-HCL PH REMARK 280 9.0, 0.1 M NACL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 102.86667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.43333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 51.43333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 102.86667 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: 9600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.6 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 -2 REMARK 465 ALA A -1 REMARK 465 HIS A 351 REMARK 465 HIS A 352 REMARK 465 HIS A 353 REMARK 465 HIS A 354 REMARK 465 HIS A 355 REMARK 465 HIS A 356 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 2038 O HOH A 2110 2.12 REMARK 500 OE1 GLU A 120 O HOH A 2069 2.13 REMARK 500 O HOH A 2114 O HOH A 2117 2.18 REMARK 500 O HOH A 2037 O HOH A 2107 2.19 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 177 CD - NE - CZ ANGL. DEV. = 9.0 DEGREES REMARK 500 ARG A 177 NE - CZ - NH1 ANGL. DEV. = 5.8 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 ASP A 98 59.44 35.95 REMARK 500 ASP A 127 88.46 -157.87 REMARK 500 ARG A 176 -110.11 -123.85 REMARK 500 VAL A 188 -34.03 -133.94 REMARK 500 SER A 226 57.04 -151.88 REMARK 500 ASP A 231 -79.34 -119.46 REMARK 500 LEU A 349 62.03 -59.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2076 DISTANCE = 7.20 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 POLYETHYLENE GLYCOL (2PE): FRAGMENTS OF PEG-200 REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 2PE A 1352 REMARK 610 2PE A 1353 REMARK 610 2PE A 1354 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 1351 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2PE A 1352 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2PE A 1353 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2PE A 1354 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1355 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1356 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1357 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OSI RELATED DB: PDB REMARK 900 STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE REMARK 900 RELATED ID: 1XAB RELATED DB: PDB REMARK 900 3-ISOPROPYLMALATE DEHYDROGENASE, LOW TEMPERATURE (150K) STRUCTURE REMARK 900 RELATED ID: 1G2U RELATED DB: PDB REMARK 900 THE STRUCTURE OF THE MUTANT, A172V, OF 3- REMARK 900 ISOPROPYLMALATEDEHYDROGENASE FROM THERMUS THERMOPHILUS HB8 : REMARK 900 ITSTHERMOSTABILITY AND STRUCTURE. REMARK 900 RELATED ID: 1DR0 RELATED DB: PDB REMARK 900 STRUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C- REMARK 900 TERMINUS, HD708 REMARK 900 RELATED ID: 1DPZ RELATED DB: PDB REMARK 900 STUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C- REMARK 900 TERMINUS, HD711 REMARK 900 RELATED ID: 1OSJ RELATED DB: PDB REMARK 900 STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE REMARK 900 RELATED ID: 1GC8 RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS 3-ISOPROPYLMALATE REMARK 900 DEHYDROGENASE MUTATED AT 172TH FROM ALA TOPHE REMARK 900 RELATED ID: 1XAA RELATED DB: PDB REMARK 900 3-ISOPROPYLMALATE DEHYDROGENASE, LOW TEMPERATURE (100K) STRUCTURE REMARK 900 RELATED ID: 1XAC RELATED DB: PDB REMARK 900 CHIMERA ISOPROPYLMALATE DEHYDROGENASE BETWEEN BACILLUS SUBTILIS (M) REMARK 900 AND THERMUS THERMOPHILUS (T) FROM N-TERMINAL: 20% T MIDDLE 20% M REMARK 900 RESIDUAL 60% T, MUTATED AT S82R. LOW TEMPERATURE (100K) STRUCTURE. REMARK 900 RELATED ID: 1DR8 RELATED DB: PDB REMARK 900 STRUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C- REMARK 900 TERMINUS, HD177 REMARK 900 RELATED ID: 1GC9 RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS 3-ISOPROPYLMALATE REMARK 900 DEHYDROGENASE MUTATED AT 172TH FROM ALA TOGLY REMARK 900 RELATED ID: 1IPD RELATED DB: PDB REMARK 900 3-ISOPROPYLMALATE DEHYDROGENASE REMARK 900 RELATED ID: 1XAD RELATED DB: PDB REMARK 900 CHIMERA ISOPROPYLMALATE DEHYDROGENASE BETWEEN BACILLUS SUBTILIS (M) REMARK 900 AND THERMUS THERMOPHILUS (T) FROM N-TERMINAL: 20% T MIDDLE 20% M REMARK 900 RESIDUAL 60% T, MUTATED AT S82R. LOW TEMPERATURE (150K) STRUCTURE. REMARK 900 RELATED ID: 1HEX RELATED DB: PDB REMARK 900 3-ISOPROPYLMALATE DEHYDROGENASE COMPLEXED WITH BETA-NICOTINAMIDE REMARK 900 ADENINE DINUCLEOTIDE, OXIDIZED(NAD+) REMARK 900 RELATED ID: 2Y41 RELATED DB: PDB REMARK 900 STRUCTURE OF ISOPROPYLMALATE DEHYDROGENASE FROM THERMUS THERMOPHILUS REMARK 900 RELATED ID: 2Y42 RELATED DB: PDB REMARK 900 STRUCTURE OF ISOPROPYLMALATE DEHYDROGENASE FROM THERMUS REMARK 900 THERMOPHILUS - COMPLEX WITH NADH AND MN REMARK 900 RELATED ID: 2Y40 RELATED DB: PDB REMARK 900 STRUCTURE OF ISOPROPYLMALATE DEHYDROGENASE FROM THERMUS THERMOPHILUS DBREF 2Y3Z A 1 345 UNP Q5SIY4 LEU3_THET8 1 345 SEQADV 2Y3Z MET A -2 UNP Q5SIY4 EXPRESSION TAG SEQADV 2Y3Z ALA A -1 UNP Q5SIY4 EXPRESSION TAG SEQADV 2Y3Z SER A 0 UNP Q5SIY4 EXPRESSION TAG SEQADV 2Y3Z ALA A 346 UNP Q5SIY4 EXPRESSION TAG SEQADV 2Y3Z ALA A 347 UNP Q5SIY4 EXPRESSION TAG SEQADV 2Y3Z ALA A 348 UNP Q5SIY4 EXPRESSION TAG SEQADV 2Y3Z LEU A 349 UNP Q5SIY4 EXPRESSION TAG SEQADV 2Y3Z GLU A 350 UNP Q5SIY4 EXPRESSION TAG SEQADV 2Y3Z HIS A 351 UNP Q5SIY4 EXPRESSION TAG SEQADV 2Y3Z HIS A 352 UNP Q5SIY4 EXPRESSION TAG SEQADV 2Y3Z HIS A 353 UNP Q5SIY4 EXPRESSION TAG SEQADV 2Y3Z HIS A 354 UNP Q5SIY4 EXPRESSION TAG SEQADV 2Y3Z HIS A 355 UNP Q5SIY4 EXPRESSION TAG SEQADV 2Y3Z HIS A 356 UNP Q5SIY4 EXPRESSION TAG SEQRES 1 A 359 MET ALA SER MET LYS VAL ALA VAL LEU PRO GLY ASP GLY SEQRES 2 A 359 ILE GLY PRO GLU VAL THR GLU ALA ALA LEU LYS VAL LEU SEQRES 3 A 359 ARG ALA LEU ASP GLU ALA GLU GLY LEU GLY LEU ALA TYR SEQRES 4 A 359 GLU VAL PHE PRO PHE GLY GLY ALA ALA ILE ASP ALA PHE SEQRES 5 A 359 GLY GLU PRO PHE PRO GLU PRO THR ARG LYS GLY VAL GLU SEQRES 6 A 359 GLU ALA GLU ALA VAL LEU LEU GLY SER VAL GLY GLY PRO SEQRES 7 A 359 LYS TRP ASP GLY LEU PRO ARG LYS ILE ARG PRO GLU THR SEQRES 8 A 359 GLY LEU LEU SER LEU ARG LYS SER GLN ASP LEU PHE ALA SEQRES 9 A 359 ASN LEU ARG PRO ALA LYS VAL PHE PRO GLY LEU GLU ARG SEQRES 10 A 359 LEU SER PRO LEU LYS GLU GLU ILE ALA ARG GLY VAL ASP SEQRES 11 A 359 VAL LEU ILE VAL ARG GLU LEU THR GLY GLY ILE TYR PHE SEQRES 12 A 359 GLY GLU PRO ARG GLY MET SER GLU ALA GLU ALA TRP ASN SEQRES 13 A 359 THR GLU ARG TYR SER LYS PRO GLU VAL GLU ARG VAL ALA SEQRES 14 A 359 ARG VAL ALA PHE GLU ALA ALA ARG LYS ARG ARG LYS HIS SEQRES 15 A 359 VAL VAL SER VAL ASP LYS ALA ASN VAL LEU GLU VAL GLY SEQRES 16 A 359 GLU PHE TRP ARG LYS THR VAL GLU GLU VAL GLY ARG GLY SEQRES 17 A 359 TYR PRO ASP VAL ALA LEU GLU HIS GLN TYR VAL ASP ALA SEQRES 18 A 359 MET ALA MET HIS LEU VAL ARG SER PRO ALA ARG PHE ASP SEQRES 19 A 359 VAL VAL VAL THR GLY ASN ILE PHE GLY ASP ILE LEU SER SEQRES 20 A 359 ASP LEU ALA SER VAL LEU PRO GLY SER LEU GLY LEU LEU SEQRES 21 A 359 PRO SER ALA SER LEU GLY ARG GLY THR PRO VAL PHE GLU SEQRES 22 A 359 PRO VAL HIS GLY SER ALA PRO ASP ILE ALA GLY LYS GLY SEQRES 23 A 359 ILE ALA ASN PRO THR ALA ALA ILE LEU SER ALA ALA MET SEQRES 24 A 359 MET LEU GLU HIS ALA PHE GLY LEU VAL GLU LEU ALA ARG SEQRES 25 A 359 LYS VAL GLU ASP ALA VAL ALA LYS ALA LEU LEU GLU THR SEQRES 26 A 359 PRO PRO PRO ASP LEU GLY GLY SER ALA GLY THR GLU ALA SEQRES 27 A 359 PHE THR ALA THR VAL LEU ARG HIS LEU ALA ALA ALA ALA SEQRES 28 A 359 LEU GLU HIS HIS HIS HIS HIS HIS HET TRS A1351 8 HET 2PE A1352 17 HET 2PE A1353 17 HET 2PE A1354 22 HET GOL A1355 6 HET GOL A1356 6 HET GOL A1357 6 HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM 2PE NONAETHYLENE GLYCOL HETNAM GOL GLYCEROL HETSYN TRS TRIS BUFFER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 TRS C4 H12 N O3 1+ FORMUL 3 2PE 3(C18 H38 O10) FORMUL 6 GOL 3(C3 H8 O3) FORMUL 9 HOH *201(H2 O) HELIX 1 1 ILE A 11 GLY A 31 1 21 HELIX 2 2 GLY A 42 GLY A 50 1 9 HELIX 3 3 PRO A 54 ALA A 64 1 11 HELIX 4 4 GLY A 74 ASP A 78 5 5 HELIX 5 5 PRO A 81 ILE A 84 5 4 HELIX 6 6 ARG A 85 GLN A 97 1 13 HELIX 7 7 LEU A 112 SER A 116 5 5 HELIX 8 8 LYS A 119 ARG A 124 1 6 HELIX 9 9 SER A 158 LYS A 175 1 18 HELIX 10 10 LEU A 189 ARG A 204 1 16 HELIX 11 11 VAL A 216 SER A 226 1 11 HELIX 12 12 PRO A 227 PHE A 230 5 4 HELIX 13 13 GLY A 236 VAL A 249 1 14 HELIX 14 14 SER A 253 LEU A 256 5 4 HELIX 15 15 ALA A 276 ALA A 280 5 5 HELIX 16 16 PRO A 287 ALA A 301 1 15 HELIX 17 17 LEU A 304 THR A 322 1 19 HELIX 18 18 PRO A 324 GLY A 328 5 5 HELIX 19 19 GLY A 332 LEU A 349 1 18 SHEET 1 AA10 LEU A 34 VAL A 38 0 SHEET 2 AA10 MET A 1 LEU A 6 1 O MET A 1 N ALA A 35 SHEET 3 AA10 ALA A 66 LEU A 69 1 O ALA A 66 N ALA A 4 SHEET 4 AA10 VAL A 268 PRO A 271 1 O PHE A 269 N LEU A 69 SHEET 5 AA10 PRO A 258 GLY A 263 -1 O SER A 259 N GLU A 270 SHEET 6 AA10 LEU A 99 LYS A 107 -1 N PHE A 100 O LEU A 262 SHEET 7 AA10 ASP A 127 GLU A 133 -1 O VAL A 128 N ALA A 106 SHEET 8 AA10 VAL A 232 THR A 235 1 O VAL A 233 N VAL A 131 SHEET 9 AA10 HIS A 179 ASP A 184 1 O HIS A 179 N VAL A 232 SHEET 10 AA10 ALA A 210 TYR A 215 1 O ALA A 210 N VAL A 180 SHEET 1 AB 2 GLY A 145 MET A 146 0 SHEET 2 AB 2 ALA A 151 TRP A 152 -1 O TRP A 152 N GLY A 145 CISPEP 1 GLU A 142 PRO A 143 0 -0.95 SITE 1 AC1 8 ARG A 104 ASP A 217 ASP A 241 ASP A 245 SITE 2 AC1 8 HOH A2115 HOH A2142 HOH A2143 HOH A2198 SITE 1 AC2 10 GLU A 171 ALA A 172 LYS A 175 ASP A 278 SITE 2 AC2 10 ALA A 280 HIS A 300 ALA A 301 PHE A 302 SITE 3 AC2 10 GLY A 303 HOH A2200 SITE 1 AC3 10 ARG A 94 ASN A 102 ARG A 104 ARG A 132 SITE 2 AC3 10 PHE A 140 VAL A 188 SER A 259 GLU A 270 SITE 3 AC3 10 GOL A1357 HOH A2142 SITE 1 AC4 14 VAL A 72 GLY A 73 GLY A 74 LEU A 254 SITE 2 AC4 14 HIS A 273 GLY A 274 SER A 275 ALA A 276 SITE 3 AC4 14 PRO A 277 ALA A 285 ASN A 286 GOL A1357 SITE 4 AC4 14 HOH A2199 HOH A2201 SITE 1 AC5 4 LYS A 76 GLY A 303 VAL A 305 HOH A2200 SITE 1 AC6 3 GLU A 212 GLN A 214 ARG A 229 SITE 1 AC7 11 SER A 71 VAL A 72 GLU A 270 PRO A 271 SITE 2 AC7 11 VAL A 272 HIS A 273 GLY A 274 2PE A1353 SITE 3 AC7 11 2PE A1354 HOH A2039 HOH A2201 CRYST1 76.480 76.480 154.300 90.00 90.00 120.00 P 32 2 1 6 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 0.013075 0.007549 0.000000 0.00000 SCALE2 0.000000 0.015098 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006481 0.00000