HEADER OXIDOREDUCTASE(CHOH(D)-NAD+(A)) 10-NOV-92 1BMD TITLE DETERMINANTS OF PROTEIN THERMOSTABILITY OBSERVED IN THE 1.9 ANGSTROMS TITLE 2 CRYSTAL STRUCTURE OF MALATE DEHYDROGENASE FROM THE THERMOPHILIC TITLE 3 BACTERIUM THERMUS FLAVUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALATE DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.1.1.37; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 EXPRESSION_SYSTEM_VECTOR_TYPE: BACTERIUM KEYWDS OXIDOREDUCTASE(CHOH(D)-NAD+(A)) EXPDTA X-RAY DIFFRACTION AUTHOR C.A.KELLY,J.J.BIRKTOFT REVDAT 7 07-FEB-24 1BMD 1 REMARK SEQADV REVDAT 6 14-AUG-19 1BMD 1 REMARK REVDAT 5 17-JUL-19 1BMD 1 REMARK REVDAT 4 29-NOV-17 1BMD 1 HELIX REVDAT 3 24-FEB-09 1BMD 1 VERSN REVDAT 2 30-SEP-03 1BMD 1 JRNL DBREF REVDAT 1 31-JUL-94 1BMD 0 JRNL AUTH C.A.KELLY,M.NISHIYAMA,Y.OHNISHI,T.BEPPU,J.J.BIRKTOFT JRNL TITL DETERMINANTS OF PROTEIN THERMOSTABILITY OBSERVED IN THE JRNL TITL 2 1.9-A CRYSTAL STRUCTURE OF MALATE DEHYDROGENASE FROM THE JRNL TITL 3 THERMOPHILIC BACTERIUM THERMUS FLAVUS. JRNL REF BIOCHEMISTRY V. 32 3913 1993 JRNL REFN ISSN 0006-2960 JRNL PMID 8471603 JRNL DOI 10.1021/BI00066A010 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.A.KELLY,S.SARFATY,M.NISHIYAMA,T.BEPPU,J.J.BIRKTOFT REMARK 1 TITL PRELIMINARY X-RAY DIFFRACTION ANALYSIS OF A CRYSTALLIZABLE REMARK 1 TITL 2 MUTANT OF MALATE DEHYDROGENASE FROM THE THERMOPHILE THERMUS REMARK 1 TITL 3 FLAVUS REMARK 1 REF J.MOL.BIOL. V. 221 383 1991 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.J.BIRKTOFT,G.RHODES,L.J.BANASZAK REMARK 1 TITL REFINED CRYSTAL STRUCTURE OF CYTOPLASMIC MALATE REMARK 1 TITL 2 DEHYDROGENASE AT 2.5 ANGSTROMS RESOLUTION REMARK 1 REF BIOCHEMISTRY V. 28 6065 1989 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 3 REMARK 1 AUTH M.NISHIYAMA,N.MATSUBARA,K.YAMAMOTO,S.IIJIMA,T.UOZUMI,T.BEPPU REMARK 1 TITL NUCLEOTIDE SEQUENCE OF THE MALATE DEHYDROGENASE GENE OF REMARK 1 TITL 2 THERMUS FLAVUS AND ITS MUTATION DIRECTING AN INCREASE IN REMARK 1 TITL 3 ENZYME ACTIVITY REMARK 1 REF J.BIOL.CHEM. V. 261 14178 1986 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 4 REMARK 1 AUTH J.J.BIRKTOFT,L.J.BANASZAK REMARK 1 TITL THE PRESENCE OF A HISTIDINE-ASPARTIC ACID PAIR IN THE ACTIVE REMARK 1 TITL 2 SITE OF 2-HYDROXYACID DEHYDROGENASES REMARK 1 REF J.BIOL.CHEM. V. 258 472 1983 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 5 REMARK 1 AUTH L.J.BANASZAK,R.A.BRADSHAW REMARK 1 TITL MALATE DEHYDROGENASES REMARK 1 REF ENZYME V. 11 369 1975 REMARK 1 REFN ISSN 0013-9432 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4976 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 288 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : NULL ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BMD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171909. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 35.75500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.49000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.79500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.49000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.75500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.79500 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 300 REMARK: THE ASYMMETRIC UNIT CONTAINS TWO SUBUNITS WHICH HAVE BEEN REMARK 300 ASSIGNED CHAIN IDENTIFIERS *A* AND *B*. THEY ARE RELATED REMARK 300 BY A NON-CRYSTALLOGRAPHIC SYMMETRY AXIS WITH A ROTATION REMARK 300 ANGLE OF 180.0 DEGREES. THE TRANSFORMATION PRESENTED ON REMARK 300 *MTRIX* RECORDS BELOW YIELDS OPTIMAL SUPERPOSITION OF REMARK 300 SUBUNIT A UPON SUBUNIT B BASED UPON ALL ALPHA CARBON ATOMS. 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: 5390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 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 50 CD GLU A 50 OE1 0.073 REMARK 500 GLU A 68 CD GLU A 68 OE1 0.067 REMARK 500 GLU A 96 CD GLU A 96 OE1 0.087 REMARK 500 GLU A 110 CD GLU A 110 OE1 0.069 REMARK 500 GLU A 198 CD GLU A 198 OE1 0.067 REMARK 500 GLU A 210 CD GLU A 210 OE1 0.072 REMARK 500 GLU A 216 CD GLU A 216 OE1 0.078 REMARK 500 GLU A 219 CD GLU A 219 OE1 0.072 REMARK 500 GLU A 262 CD GLU A 262 OE1 0.079 REMARK 500 GLU A 281 CD GLU A 281 OE1 0.074 REMARK 500 GLU A 300 CD GLU A 300 OE2 0.066 REMARK 500 GLU A 303 CD GLU A 303 OE2 0.067 REMARK 500 GLU A 306 CD GLU A 306 OE1 0.075 REMARK 500 GLU A 313 CD GLU A 313 OE2 0.070 REMARK 500 GLU A 324 CD GLU A 324 OE2 0.090 REMARK 500 GLU B 27 CD GLU B 27 OE2 -0.069 REMARK 500 GLU B 50 CD GLU B 50 OE2 0.070 REMARK 500 GLU B 68 CD GLU B 68 OE1 0.080 REMARK 500 GLU B 96 CD GLU B 96 OE1 0.090 REMARK 500 GLU B 117 CD GLU B 117 OE2 0.070 REMARK 500 GLU B 210 CD GLU B 210 OE1 0.083 REMARK 500 GLU B 216 CD GLU B 216 OE1 0.069 REMARK 500 GLU B 251 CD GLU B 251 OE2 -0.076 REMARK 500 GLU B 262 CD GLU B 262 OE2 0.094 REMARK 500 GLU B 303 CD GLU B 303 OE2 0.066 REMARK 500 GLU B 306 CD GLU B 306 OE2 0.081 REMARK 500 GLU B 313 CD GLU B 313 OE1 0.083 REMARK 500 GLU B 324 CD GLU B 324 OE1 0.087 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 5 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 5 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES REMARK 500 ASP A 71 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ASP A 71 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ASP A 72 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 72 CB - CG - OD2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 98 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ASP A 122 CB - CG - OD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 PRO A 144 C - N - CD ANGL. DEV. = -14.3 DEGREES REMARK 500 ASP A 175 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP A 193 CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ASP A 200 CB - CG - OD1 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 206 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 ASP A 214 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 214 CB - CG - OD2 ANGL. DEV. = -8.2 DEGREES REMARK 500 ARG A 237 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 237 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ASP A 264 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 264 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 297 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 297 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 321 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP B 32 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP B 58 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP B 71 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP B 71 CB - CG - OD2 ANGL. DEV. = -7.9 DEGREES REMARK 500 ASP B 74 CB - CG - OD1 ANGL. DEV. = -7.9 DEGREES REMARK 500 ASP B 74 CB - CG - OD2 ANGL. DEV. = 8.4 DEGREES REMARK 500 ASP B 79 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 PRO B 90 C - N - CD ANGL. DEV. = -15.8 DEGREES REMARK 500 ARG B 91 NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES REMARK 500 GLU B 96 N - CA - CB ANGL. DEV. = -19.2 DEGREES REMARK 500 ARG B 98 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ASP B 122 CB - CG - OD2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ASP B 122 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 PRO B 144 C - N - CD ANGL. DEV. = -12.9 DEGREES REMARK 500 ARG B 178 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 ASP B 193 CB - CG - OD1 ANGL. DEV. = 8.9 DEGREES REMARK 500 ASP B 193 CB - CG - OD2 ANGL. DEV. = -9.5 DEGREES REMARK 500 LYS B 220 N - CA - CB ANGL. DEV. = 11.9 DEGREES REMARK 500 ARG B 254 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP B 293 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 311 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 97 -75.04 -46.09 REMARK 500 LEU A 258 -60.14 -92.02 REMARK 500 ALA B 143 65.70 -119.73 REMARK 500 SER B 187 -166.06 -165.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 HIS A 186 10.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 334 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 334 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE NUMBERING SYSTEM IS THE SAME AS THAT USED FOR THE REMARK 999 CYTOPLASMIC MALATE DEHYDROGENASE STRUCTURE. THE DELETION REMARK 999 REGIONS IN TMDH, 201 - 204, 213, AND 276, LEAD TO REMARK 999 DISCONTINUITIES IN THE TMDH NUMBERING. HOWEVER, THERE ARE REMARK 999 NO BREAKS IN THE PEPTIDE CHAIN. REMARK 999 REMARK 999 SEQUENCE ADVISORY NOTICE: REMARK 999 DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. REMARK 999 REMARK 999 SWISS-PROT ENTRY NAME: MDH_THEFL REMARK 999 REMARK 999 SWISS-PROT RESIDUE PDB SEQRES REMARK 999 NAME NUMBER NAME CHAIN SEQ/INSERT CODE REMARK 999 LYS 75 ASP A 74 REMARK 999 LYS 75 ASP B 74 DBREF 1BMD A 0 332 UNP P10584 MDH_THETH 1 327 DBREF 1BMD B 0 332 UNP P10584 MDH_THETH 1 327 SEQADV 1BMD ASP A 74 UNP P10584 LYS 75 CONFLICT SEQADV 1BMD ASP B 74 UNP P10584 LYS 75 CONFLICT SEQRES 1 A 327 MET LYS ALA PRO VAL ARG VAL ALA VAL THR GLY ALA ALA SEQRES 2 A 327 GLY GLN ILE GLY TYR SER LEU LEU PHE ARG ILE ALA ALA SEQRES 3 A 327 GLY GLU MET LEU GLY LYS ASP GLN PRO VAL ILE LEU GLN SEQRES 4 A 327 LEU LEU GLU ILE PRO GLN ALA MET LYS ALA LEU GLU GLY SEQRES 5 A 327 VAL VAL MET GLU LEU GLU ASP CYS ALA PHE PRO LEU LEU SEQRES 6 A 327 ALA GLY LEU GLU ALA THR ASP ASP PRO ASP VAL ALA PHE SEQRES 7 A 327 LYS ASP ALA ASP TYR ALA LEU LEU VAL GLY ALA ALA PRO SEQRES 8 A 327 ARG LYS ALA GLY MET GLU ARG ARG ASP LEU LEU GLN VAL SEQRES 9 A 327 ASN GLY LYS ILE PHE THR GLU GLN GLY ARG ALA LEU ALA SEQRES 10 A 327 GLU VAL ALA LYS LYS ASP VAL LYS VAL LEU VAL VAL GLY SEQRES 11 A 327 ASN PRO ALA ASN THR ASN ALA LEU ILE ALA TYR LYS ASN SEQRES 12 A 327 ALA PRO GLY LEU ASN PRO ARG ASN PHE THR ALA MET THR SEQRES 13 A 327 ARG LEU ASP HIS ASN ARG ALA LYS ALA GLN LEU ALA LYS SEQRES 14 A 327 LYS THR GLY THR GLY VAL ASP ARG ILE ARG ARG MET THR SEQRES 15 A 327 VAL TRP GLY ASN HIS SER SER THR MET PHE PRO ASP LEU SEQRES 16 A 327 PHE HIS ALA GLU VAL ASP GLY ARG PRO ALA LEU GLU LEU SEQRES 17 A 327 VAL ASP MET GLU TRP TYR GLU LYS VAL PHE ILE PRO THR SEQRES 18 A 327 VAL ALA GLN ARG GLY ALA ALA ILE ILE GLN ALA ARG GLY SEQRES 19 A 327 ALA SER SER ALA ALA SER ALA ALA ASN ALA ALA ILE GLU SEQRES 20 A 327 HIS ILE ARG ASP TRP ALA LEU GLY THR PRO GLU GLY ASP SEQRES 21 A 327 TRP VAL SER MET ALA VAL PRO SER GLN GLY GLU TYR GLY SEQRES 22 A 327 ILE PRO GLU GLY ILE VAL TYR SER PHE PRO VAL THR ALA SEQRES 23 A 327 LYS ASP GLY ALA TYR ARG VAL VAL GLU GLY LEU GLU ILE SEQRES 24 A 327 ASN GLU PHE ALA ARG LYS ARG MET GLU ILE THR ALA GLN SEQRES 25 A 327 GLU LEU LEU ASP GLU MET GLU GLN VAL LYS ALA LEU GLY SEQRES 26 A 327 LEU ILE SEQRES 1 B 327 MET LYS ALA PRO VAL ARG VAL ALA VAL THR GLY ALA ALA SEQRES 2 B 327 GLY GLN ILE GLY TYR SER LEU LEU PHE ARG ILE ALA ALA SEQRES 3 B 327 GLY GLU MET LEU GLY LYS ASP GLN PRO VAL ILE LEU GLN SEQRES 4 B 327 LEU LEU GLU ILE PRO GLN ALA MET LYS ALA LEU GLU GLY SEQRES 5 B 327 VAL VAL MET GLU LEU GLU ASP CYS ALA PHE PRO LEU LEU SEQRES 6 B 327 ALA GLY LEU GLU ALA THR ASP ASP PRO ASP VAL ALA PHE SEQRES 7 B 327 LYS ASP ALA ASP TYR ALA LEU LEU VAL GLY ALA ALA PRO SEQRES 8 B 327 ARG LYS ALA GLY MET GLU ARG ARG ASP LEU LEU GLN VAL SEQRES 9 B 327 ASN GLY LYS ILE PHE THR GLU GLN GLY ARG ALA LEU ALA SEQRES 10 B 327 GLU VAL ALA LYS LYS ASP VAL LYS VAL LEU VAL VAL GLY SEQRES 11 B 327 ASN PRO ALA ASN THR ASN ALA LEU ILE ALA TYR LYS ASN SEQRES 12 B 327 ALA PRO GLY LEU ASN PRO ARG ASN PHE THR ALA MET THR SEQRES 13 B 327 ARG LEU ASP HIS ASN ARG ALA LYS ALA GLN LEU ALA LYS SEQRES 14 B 327 LYS THR GLY THR GLY VAL ASP ARG ILE ARG ARG MET THR SEQRES 15 B 327 VAL TRP GLY ASN HIS SER SER THR MET PHE PRO ASP LEU SEQRES 16 B 327 PHE HIS ALA GLU VAL ASP GLY ARG PRO ALA LEU GLU LEU SEQRES 17 B 327 VAL ASP MET GLU TRP TYR GLU LYS VAL PHE ILE PRO THR SEQRES 18 B 327 VAL ALA GLN ARG GLY ALA ALA ILE ILE GLN ALA ARG GLY SEQRES 19 B 327 ALA SER SER ALA ALA SER ALA ALA ASN ALA ALA ILE GLU SEQRES 20 B 327 HIS ILE ARG ASP TRP ALA LEU GLY THR PRO GLU GLY ASP SEQRES 21 B 327 TRP VAL SER MET ALA VAL PRO SER GLN GLY GLU TYR GLY SEQRES 22 B 327 ILE PRO GLU GLY ILE VAL TYR SER PHE PRO VAL THR ALA SEQRES 23 B 327 LYS ASP GLY ALA TYR ARG VAL VAL GLU GLY LEU GLU ILE SEQRES 24 B 327 ASN GLU PHE ALA ARG LYS ARG MET GLU ILE THR ALA GLN SEQRES 25 B 327 GLU LEU LEU ASP GLU MET GLU GLN VAL LYS ALA LEU GLY SEQRES 26 B 327 LEU ILE HET NAD A 334 44 HET NAD B 334 44 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 5 HOH *288(H2 O) HELIX 1 BA GLN A 14 ALA A 24 1 11 HELIX 2 CA PRO A 43 GLU A 57 1 15 HELIX 3 CPA PRO A 73 ALA A 76 1 4 HELIX 4 DEA ARG A 97 VAL A 118 1 22 HELIX 5 1FA ALA A 132 LYS A 141 1 10 HELIX 6 2FA ARG A 156 THR A 170 1 15 HELIX 7 GPA ALA A 208 VAL A 212 1 5 HELIX 8 1GA MET A 215 ALA A 227 1 13 HELIX 9 2GA ARG A 229 ARG A 237 1 9 HELIX 10 3GA ALA A 242 ALA A 257 1 16 HELIX 11 HA GLU A 306 ALA A 328 1 23 HELIX 12 BB GLN B 14 ALA B 24 1 11 HELIX 13 CB PRO B 43 GLU B 57 1 15 HELIX 14 CPB PRO B 73 ALA B 76 1 4 HELIX 15 DEB ARG B 97 VAL B 118 1 22 HELIX 16 1FB ALA B 132 LYS B 141 1 10 HELIX 17 2FB ARG B 156 THR B 170 1 15 HELIX 18 GPB ALA B 208 VAL B 212 1 5 HELIX 19 1GB MET B 215 ALA B 227 1 13 HELIX 20 2GB ARG B 229 ARG B 237 1 9 HELIX 21 3GB ALA B 242 LEU B 258 1 17 HELIX 22 HB GLU B 306 ALA B 328 1 23 SHEET 1 S1A 6 LEU A 64 THR A 70 0 SHEET 2 S1A 6 VAL A 35 LEU A 40 1 SHEET 3 S1A 6 VAL A 4 THR A 9 1 SHEET 4 S1A 6 TYR A 82 LEU A 85 1 SHEET 5 S1A 6 LYS A 124 VAL A 127 1 SHEET 6 S1A 6 PHE A 151 ALA A 153 1 SHEET 1 S2A 3 ILE A 177 TRP A 183 0 SHEET 2 S2A 3 PHE A 191 VAL A 199 -1 SHEET 3 S2A 3 ARG A 206 PRO A 207 -1 SHEET 1 S3A 3 VAL A 266 PRO A 271 0 SHEET 2 S3A 3 VAL A 284 LYS A 292 -1 SHEET 3 S3A 3 ALA A 295 VAL A 298 -1 SHEET 1 S1B 6 LEU B 64 THR B 70 0 SHEET 2 S1B 6 VAL B 35 LEU B 40 1 SHEET 3 S1B 6 VAL B 4 THR B 9 1 SHEET 4 S1B 6 TYR B 82 LEU B 85 1 SHEET 5 S1B 6 LYS B 124 VAL B 127 1 SHEET 6 S1B 6 PHE B 151 ALA B 153 1 SHEET 1 S2B 3 ILE B 177 TRP B 183 0 SHEET 2 S2B 3 PHE B 191 VAL B 199 -1 SHEET 3 S2B 3 ARG B 206 PRO B 207 -1 SHEET 1 S3B 3 VAL B 266 PRO B 271 0 SHEET 2 S3B 3 VAL B 284 LYS B 292 -1 SHEET 3 S3B 3 ALA B 295 VAL B 298 -1 CISPEP 1 ASN A 130 PRO A 131 0 -5.12 CISPEP 2 ASN B 130 PRO B 131 0 -3.28 SITE 1 AC1 18 GLY A 10 GLY A 13 GLN A 14 ILE A 15 SITE 2 AC1 18 GLU A 41 ILE A 42 VAL A 86 GLY A 87 SITE 3 AC1 18 ALA A 88 GLN A 111 VAL A 128 GLY A 129 SITE 4 AC1 18 ASN A 130 MET A 154 HIS A 186 HOH A 342 SITE 5 AC1 18 HOH A 356 HOH A 430 SITE 1 AC2 20 GLY B 10 GLY B 13 GLN B 14 ILE B 15 SITE 2 AC2 20 LEU B 40 GLU B 41 ILE B 42 VAL B 86 SITE 3 AC2 20 GLY B 87 ALA B 88 GLN B 111 VAL B 128 SITE 4 AC2 20 GLY B 129 ASN B 130 MET B 154 HIS B 186 SITE 5 AC2 20 HOH B 345 HOH B 357 HOH B 437 HOH B 491 CRYST1 71.510 87.590 118.980 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013984 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011417 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008405 0.00000 MTRIX1 1 -0.606800 0.002100 -0.794800 81.10670 1 MTRIX2 1 0.003600 -1.000000 -0.005500 50.92750 1 MTRIX3 1 -0.794800 -0.006200 0.606800 40.36920 1