HEADER OXIDOREDUCTASE(NAD(A)-CHOH(D)) 16-FEB-93 1BDM
TITLE THE STRUCTURE AT 1.8 ANGSTROMS RESOLUTION OF A SINGLE SITE MUTANT
TITLE 2 (T189I) OF MALATE DEHYDROGENASE FROM THERMUS FLAVUS WITH INCREASED
TITLE 3 ENZYMATIC ACTIVITY
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(NAD(A)-CHOH(D))
EXPDTA X-RAY DIFFRACTION
AUTHOR C.A.KELLY,J.J.BIRKTOFT
REVDAT 6 07-FEB-24 1BDM 1 REMARK SEQADV
REVDAT 5 29-NOV-17 1BDM 1 HELIX
REVDAT 4 24-FEB-09 1BDM 1 VERSN
REVDAT 3 28-DEC-04 1BDM 1 REMARK
REVDAT 2 21-DEC-04 1BDM 1 TITLE KEYWDS EXPDTA JRNL
REVDAT 1 20-DEC-94 1BDM 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 M.NISHIYAMA,K.SHIMADA,S.HORINOUCHI,T.BEPPU
REMARK 1 TITL ROLE OF THREONINE 190 IN MODULATING THE CATALYTIC FUNCTION
REMARK 1 TITL 2 OF MALATE DEHYDROGENASE FROM A THERMOPHILE THERMUS FLAVUS
REMARK 1 REF J.BIOL.CHEM. V. 266 14294 1991
REMARK 1 REFN ISSN 0021-9258
REMARK 1 REFERENCE 3
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 4
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 5
REMARK 1 AUTH N.J.OPPENHEIMER
REMARK 1 TITL CHEMISTRY AND SOLUTION CONFORMATION OF THE PYRIDINE
REMARK 1 TITL 2 COENZYMES
REMARK 1 EDIT J.EVERSE, B.ANDERSON, K.-S.YOU
REMARK 1 REF THE PYRIDINE NUCLEOTIDE 51 1982
REMARK 1 REF 2 COENZYMES
REMARK 1 PUBL ACADEMIC PRESS, NEW YORK
REMARK 1 REFN
REMARK 1 REFERENCE 6
REMARK 1 AUTH L.J.BANASZAK,R.A.BRADSHAW
REMARK 1 TITL MALATE DEHYDROGENASE
REMARK 1 EDIT P.D.BOYER
REMARK 1 REF THE ENZYMES,THIRD EDITION V. 11A 369 1975
REMARK 1 PUBL ACADEMIC PRESS,NEW YORK
REMARK 1 REFN
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : NULL
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING SET) : 0.169
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 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4895
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 90
REMARK 3 SOLVENT ATOMS : 202
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.014
REMARK 3 BOND ANGLES (DEGREES) : 2.770
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1BDM 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_1000171628.
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: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 53.86
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67
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 35.87500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.48500
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.32000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.48500
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.87500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.32000
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 PROVIDED ON
REMARK 300 THE *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: 5420 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 24680 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 LYS A 92
REMARK 465 ALA A 93
REMARK 465 GLY A 94
REMARK 465 MET A 95
REMARK 465 GLU A 96
REMARK 465 ARG A 97
REMARK 465 ARG A 98
REMARK 465 ASP A 99
REMARK 465 LEU A 100
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 ARG A 91 CA C O CB CG CD NE
REMARK 470 ARG A 91 CZ NH1 NH2
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 0.068
REMARK 500 GLU A 55 CD GLU A 55 OE1 0.067
REMARK 500 GLU A 68 CD GLU A 68 OE1 0.066
REMARK 500 GLU A 110 CD GLU A 110 OE1 0.084
REMARK 500 GLU A 117 CD GLU A 117 OE2 0.077
REMARK 500 GLU A 198 CD GLU A 198 OE1 0.083
REMARK 500 GLU A 210 CD GLU A 210 OE1 0.086
REMARK 500 GLU A 251 CD GLU A 251 OE1 0.081
REMARK 500 GLU A 275 CD GLU A 275 OE1 0.081
REMARK 500 GLU A 281 CD GLU A 281 OE1 0.070
REMARK 500 GLU A 306 CD GLU A 306 OE2 0.083
REMARK 500 GLU A 313 CD GLU A 313 OE2 0.070
REMARK 500 GLU A 318 CD GLU A 318 OE1 0.076
REMARK 500 GLU A 324 CD GLU A 324 OE2 0.076
REMARK 500 GLU B 41 CD GLU B 41 OE2 0.071
REMARK 500 GLU B 50 CD GLU B 50 OE2 0.068
REMARK 500 GLU B 55 CD GLU B 55 OE1 0.071
REMARK 500 GLU B 57 CD GLU B 57 OE2 -0.070
REMARK 500 GLU B 68 CD GLU B 68 OE1 0.088
REMARK 500 GLU B 96 CD GLU B 96 OE1 0.076
REMARK 500 GLU B 110 CD GLU B 110 OE1 0.069
REMARK 500 GLU B 117 CD GLU B 117 OE2 0.074
REMARK 500 GLU B 210 CD GLU B 210 OE1 0.081
REMARK 500 GLU B 216 CD GLU B 216 OE1 0.078
REMARK 500 GLU B 262 CD GLU B 262 OE2 0.077
REMARK 500 GLU B 306 CD GLU B 306 OE1 0.083
REMARK 500 GLU B 313 CD GLU B 313 OE1 0.086
REMARK 500 GLU B 318 CD GLU B 318 OE2 0.070
REMARK 500 GLU B 322 CD GLU B 322 OE2 0.068
REMARK 500 GLU B 324 CD GLU B 324 OE1 0.074
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 - NH2 ANGL. DEV. = 4.0 DEGREES
REMARK 500 ASP A 58 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 ASP A 58 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES
REMARK 500 LEU A 67 CB - CA - C ANGL. DEV. = -13.0 DEGREES
REMARK 500 ASP A 71 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES
REMARK 500 ASP A 72 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES
REMARK 500 ASP A 74 CB - CG - OD1 ANGL. DEV. = -9.1 DEGREES
REMARK 500 ASP A 74 CB - CG - OD2 ANGL. DEV. = 7.2 DEGREES
REMARK 500 PRO A 144 C - N - CD ANGL. DEV. = -15.6 DEGREES
REMARK 500 ARG A 156 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 ASP A 193 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES
REMARK 500 ASP A 193 CB - CG - OD2 ANGL. DEV. = -7.7 DEGREES
REMARK 500 ASP A 200 CB - CG - OD1 ANGL. DEV. = -8.0 DEGREES
REMARK 500 ARG A 206 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES
REMARK 500 ASP A 214 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES
REMARK 500 ASP A 214 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES
REMARK 500 MET A 215 CG - SD - CE ANGL. DEV. = -15.2 DEGREES
REMARK 500 LYS A 220 CA - CB - CG ANGL. DEV. = -16.6 DEGREES
REMARK 500 ARG A 237 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES
REMARK 500 ASP A 264 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES
REMARK 500 ASP A 264 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES
REMARK 500 ASP A 293 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES
REMARK 500 ASP A 321 CB - CG - OD1 ANGL. DEV. = -6.5 DEGREES
REMARK 500 VAL B 35 CG1 - CB - CG2 ANGL. DEV. = -10.1 DEGREES
REMARK 500 ASP B 71 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES
REMARK 500 ASP B 71 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES
REMARK 500 ASP B 72 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES
REMARK 500 ASP B 74 CB - CG - OD1 ANGL. DEV. = -6.4 DEGREES
REMARK 500 ASP B 74 CB - CG - OD2 ANGL. DEV. = 7.4 DEGREES
REMARK 500 GLU B 96 N - CA - CB ANGL. DEV. = -13.3 DEGREES
REMARK 500 ARG B 149 NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES
REMARK 500 ARG B 149 NE - CZ - NH2 ANGL. DEV. = 5.6 DEGREES
REMARK 500 ARG B 161 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES
REMARK 500 ARG B 161 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES
REMARK 500 ARG B 178 CD - NE - CZ ANGL. DEV. = 11.3 DEGREES
REMARK 500 ARG B 178 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES
REMARK 500 ARG B 179 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES
REMARK 500 ASP B 193 CB - CG - OD1 ANGL. DEV. = 7.9 DEGREES
REMARK 500 ASP B 193 CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES
REMARK 500 ASP B 200 CB - CG - OD1 ANGL. DEV. = -6.4 DEGREES
REMARK 500 ASP B 264 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 MET B 323 CG - SD - CE ANGL. DEV. = -12.2 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 LEU A 258 -69.32 -91.29
REMARK 500 TYR A 277 15.09 53.80
REMARK 500 TYR B 277 17.43 55.89
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN
REMARK 600
REMARK 600 WHILE THE ENZYME WAS CRYSTALLIZED AT PH 7.5 IN THE PRESENCE
REMARK 600 OF THE REDUCED COENZYME NADH, THE ELECTRON DENSITY MAP WAS
REMARK 600 BEST FIT BY THE MODIFIED COENZYME REFERRED TO AS NADHX.
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAX A 334
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAX 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-T189I, 201 - 204, 213 AND 276, LEAD TO
REMARK 999 DISCONTINUITIES IN THE TMDH NUMBERING; HOWEVER, THESE DO
REMARK 999 NOT REPRESENT 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
REMARK 999 NAME NUMBER NAME CHAIN SEQ/INSERT CODE
REMARK 999 LYS 75 ASP A 74
REMARK 999
REMARK 999 CROSS REFERENCE TO SEQUENCE DATABASE
REMARK 999 SWISS-PROT ENTRY NAME PDB ENTRY CHAIN NAME
REMARK 999 MDH_THEFL B
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
REMARK 999 NAME NUMBER NAME CHAIN SEQ/INSERT CODE
REMARK 999 LYS 75 ASP B 74
REMARK 999
REMARK 999 THE SEQUENCE PRESENTED IN THE ENTRY FITS THE OBSERVED
REMARK 999 DENSITY BETTER THAN THE PUBLISHED SEQUENCE.
DBREF 1BDM A 0 332 UNP P10584 MDH_THETH 1 327
DBREF 1BDM B 0 332 UNP P10584 MDH_THETH 1 327
SEQADV 1BDM ASP A 74 UNP P10584 LYS 75 CONFLICT
SEQADV 1BDM ILE A 189 UNP P10584 THR 190 CONFLICT
SEQADV 1BDM ASP B 74 UNP P10584 LYS 75 CONFLICT
SEQADV 1BDM ILE B 189 UNP P10584 THR 190 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 ILE 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 ILE 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 NAX A 334 45
HET NAX B 334 45
HETNAM NAX BETA-6-HYDROXY-1,4,5,6-TETRHYDRONICOTINAMIDE ADENINE
HETNAM 2 NAX DINUCLEOTIDE
FORMUL 3 NAX 2(C21 H31 N7 O15 P2)
FORMUL 5 HOH *202(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 LEU A 101 VAL A 118 1 18
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 -4.84
CISPEP 2 ASN B 130 PRO B 131 0 -3.39
SITE 1 AC1 23 GLY A 10 GLY A 13 GLN A 14 ILE A 15
SITE 2 AC1 23 GLU A 41 ILE A 42 VAL A 86 GLY A 87
SITE 3 AC1 23 ALA A 88 GLN A 111 VAL A 128 GLY A 129
SITE 4 AC1 23 ASN A 130 MET A 154 HIS A 186 ALA A 245
SITE 5 AC1 23 HOH A 767 HOH A 795 HOH A 904 HOH A 907
SITE 6 AC1 23 HOH A 913 HOH A 916 HOH A 950
SITE 1 AC2 22 GLY B 10 GLY B 13 GLN B 14 ILE B 15
SITE 2 AC2 22 GLU B 41 ILE B 42 VAL B 86 GLY B 87
SITE 3 AC2 22 ALA B 88 ILE B 107 GLN B 111 VAL B 128
SITE 4 AC2 22 GLY B 129 ASN B 130 MET B 154 HIS B 186
SITE 5 AC2 22 ALA B 245 HOH B 765 HOH B 784 HOH B 866
SITE 6 AC2 22 HOH B 922 HOH B 933
CRYST1 71.750 88.640 118.970 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 0.013937 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011282 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008405 0.00000
MTRIX1 1 -0.609800 0.001100 -0.792600 81.32230 1
MTRIX2 1 0.006700 -1.000000 -0.006600 51.70460 1
MTRIX3 1 -0.792600 -0.009400 0.609700 40.40520 1
(ATOM LINES ARE NOT SHOWN.)
END
