HEADER OXIDOREDUCTASE 17-JUN-14 4TRO
TITLE STRUCTURE OF THE ENOYL-ACP REDUCTASE OF MYCOBACTERIUM TUBERCULOSIS
TITLE 2 INHA, INHIBITED WITH THE ACTIVE METABOLITE OF ISONIAZID
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH];
COMPND 3 CHAIN: A;
COMPND 4 EC: 1.3.1.9;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS;
SOURCE 3 ORGANISM_TAXID: 1773;
SOURCE 4 GENE: INHA;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)
KEYWDS ISONIAZID, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.CHOLLET,S.JULIEN,L.MOUREY,L.MAVEYRAUD
REVDAT 3 20-DEC-23 4TRO 1 REMARK
REVDAT 2 17-JUN-15 4TRO 1 JRNL
REVDAT 1 29-APR-15 4TRO 0
JRNL AUTH A.CHOLLET,L.MOUREY,C.LHERBET,A.DELBOT,S.JULIEN,M.BALTAS,
JRNL AUTH 2 J.BERNADOU,G.PRATVIEL,L.MAVEYRAUD,V.BERNARDES-GENISSON
JRNL TITL CRYSTAL STRUCTURE OF THE ENOYL-ACP REDUCTASE OF
JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS (INHA) IN THE APO-FORM AND IN
JRNL TITL 3 COMPLEX WITH THE ACTIVE METABOLITE OF ISONIAZID PRE-FORMED
JRNL TITL 4 BY A BIOMIMETIC APPROACH.
JRNL REF J.STRUCT.BIOL. V. 190 328 2015
JRNL REFN ESSN 1095-8657
JRNL PMID 25891098
JRNL DOI 10.1016/J.JSB.2015.04.008
REMARK 2
REMARK 2 RESOLUTION. 1.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0071
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) : 1.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 3 NUMBER OF REFLECTIONS : 73178
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) : 0.123
REMARK 3 R VALUE (WORKING SET) : 0.121
REMARK 3 FREE R VALUE : 0.151
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 3858
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) : 1.40
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44
REMARK 3 REFLECTION IN BIN (WORKING SET) : 5270
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.50
REMARK 3 BIN R VALUE (WORKING SET) : 0.1940
REMARK 3 BIN FREE R VALUE SET COUNT : 264
REMARK 3 BIN FREE R VALUE : 0.2020
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1994
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 141
REMARK 3 SOLVENT ATOMS : 266
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.76
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.61000
REMARK 3 B22 (A**2) : 0.61000
REMARK 3 B33 (A**2) : -1.98000
REMARK 3 B12 (A**2) : 0.30000
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): 0.038
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.040
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.027
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.568
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.983
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.976
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2274 ; 0.021 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 2162 ; 0.004 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3113 ; 2.174 ; 2.007
REMARK 3 BOND ANGLES OTHERS (DEGREES): 4965 ; 1.419 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 286 ; 5.691 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 86 ;33.759 ;23.837
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 348 ;12.009 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;17.008 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 352 ; 0.199 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2694 ; 0.010 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 508 ; 0.004 ; 0.020
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): 1120 ; 7.479 ;11.704
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1119 ; 7.445 ;11.687
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1414 ; 7.939 ;16.976
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1415 ; 7.948 ;16.987
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1154 ;23.874 ;15.832
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1155 ;23.867 ;15.850
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1700 ;22.377 ;21.023
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2721 ;16.388 ;38.497
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2605 ;16.615 ;37.429
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4435 ; 6.535 ; 3.000
REMARK 3 SPHERICITY; FREE ATOMS (A**2): 95 ;41.249 ; 5.000
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4556 ;37.630 ; 5.000
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 : BABINET MODEL WITH MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
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 4TRO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUN-14.
REMARK 100 THE DEPOSITION ID IS D_1000200536.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-DEC-12
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.8
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SOLEIL
REMARK 200 BEAMLINE : PROXIMA 1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.98011
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77041
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400
REMARK 200 RESOLUTION RANGE LOW (A) : 48.720
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 200 DATA REDUNDANCY : 10.70
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.05500
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.1100
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2
REMARK 200 DATA REDUNDANCY IN SHELL : 10.40
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.716
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: 1ENY
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 63.32
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.35
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 8-10 % (V/V) 2-METHYL-2,4-PENTANEDIOL,
REMARK 280 0.1 M SODIUM CITRATE, 0.1 M NA HEPES, PH 6.8, VAPOR DIFFUSION,
REMARK 280 HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2
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 -X,-Y,Z
REMARK 290 5555 Y,-X+Y,Z+2/3
REMARK 290 6555 X-Y,X,Z+1/3
REMARK 290 7555 Y,X,-Z+2/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+1/3
REMARK 290 10555 -Y,-X,-Z+2/3
REMARK 290 11555 -X+Y,Y,-Z
REMARK 290 12555 X,X-Y,-Z+1/3
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 93.16800
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 46.58400
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 93.16800
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 46.58400
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 93.16800
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 46.58400
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 93.16800
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 46.58400
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: TETRAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 30900 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 33080 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -170.0 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 48.71700
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -84.38032
REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 0.00000
REMARK 350 BIOMT2 3 -0.866025 0.500000 0.000000 0.00000
REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 46.58400
REMARK 350 BIOMT1 4 0.500000 0.866025 0.000000 48.71700
REMARK 350 BIOMT2 4 0.866025 -0.500000 0.000000 -84.38032
REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 46.58400
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 435 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 447 LIES ON A SPECIAL POSITION.
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 1
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 THR A 2 OG1 CG2
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 SER A 129 CB SER A 129 OG -0.101
REMARK 500 GLU A 209 CD GLU A 209 OE2 -0.117
REMARK 500 GLU A 210 CB GLU A 210 CG -0.206
REMARK 500 GLU A 210 CD GLU A 210 OE2 0.067
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 PHE A 149 N - CA - C ANGL. DEV. = -16.6 DEGREES
REMARK 500 ARG A 153 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES
REMARK 500 MET A 155 CA - CB - CG ANGL. DEV. = 12.7 DEGREES
REMARK 500 MET A 155 CG - SD - CE ANGL. DEV. = -12.5 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 ILE A 16 -32.17 -131.67
REMARK 500 ASP A 42 -62.63 70.70
REMARK 500 ALA A 124 -55.48 -127.11
REMARK 500 ALA A 157 -41.78 72.14
REMARK 500 ASN A 159 -117.55 44.06
REMARK 500 ALA A 260 73.64 -102.09
REMARK 500
REMARK 500 REMARK: NULL
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 EPE A 304
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 NA A 310 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLY A 141 O
REMARK 620 2 ASP A 248 OD1 136.7
REMARK 620 3 HOH A 470 O 95.0 121.5
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 309 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 223 O
REMARK 620 2 GLN A 224 O 79.1
REMARK 620 3 ALA A 226 O 94.1 104.7
REMARK 620 4 HOH A 612 O 95.3 80.9 169.9
REMARK 620 5 HOH A 627 O 157.7 79.0 87.4 85.3
REMARK 620 6 HOH A 666 O 105.0 163.8 90.8 83.1 97.2
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 NAD A 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZID A 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 304
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 306
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 307
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 308
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 309
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 310
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4TRM RELATED DB: PDB
REMARK 900 4TRM CONTAINS THE NATIVE APO STRUCTURE
REMARK 900 RELATED ID: 4TRN RELATED DB: PDB
REMARK 900 4TRN CONTAINS THE SAME PROTEIN COMPLEXED WITH NADH
DBREF 4TRO A 1 269 UNP M9TGV3 M9TGV3_MYCTX 1 269
SEQRES 1 A 269 MET THR GLY LEU LEU ASP GLY LYS ARG ILE LEU VAL SER
SEQRES 2 A 269 GLY ILE ILE THR ASP SER SER ILE ALA PHE HIS ILE ALA
SEQRES 3 A 269 ARG VAL ALA GLN GLU GLN GLY ALA GLN LEU VAL LEU THR
SEQRES 4 A 269 GLY PHE ASP ARG LEU ARG LEU ILE GLN ARG ILE THR ASP
SEQRES 5 A 269 ARG LEU PRO ALA LYS ALA PRO LEU LEU GLU LEU ASP VAL
SEQRES 6 A 269 GLN ASN GLU GLU HIS LEU ALA SER LEU ALA GLY ARG VAL
SEQRES 7 A 269 THR GLU ALA ILE GLY ALA GLY ASN LYS LEU ASP GLY VAL
SEQRES 8 A 269 VAL HIS SER ILE GLY PHE MET PRO GLN THR GLY MET GLY
SEQRES 9 A 269 ILE ASN PRO PHE PHE ASP ALA PRO TYR ALA ASP VAL SER
SEQRES 10 A 269 LYS GLY ILE HIS ILE SER ALA TYR SER TYR ALA SER MET
SEQRES 11 A 269 ALA LYS ALA LEU LEU PRO ILE MET ASN PRO GLY GLY SER
SEQRES 12 A 269 ILE VAL GLY MET ASP PHE ASP PRO SER ARG ALA MET PRO
SEQRES 13 A 269 ALA TYR ASN TRP MET THR VAL ALA LYS SER ALA LEU GLU
SEQRES 14 A 269 SER VAL ASN ARG PHE VAL ALA ARG GLU ALA GLY LYS TYR
SEQRES 15 A 269 GLY VAL ARG SER ASN LEU VAL ALA ALA GLY PRO ILE ARG
SEQRES 16 A 269 THR LEU ALA MET SER ALA ILE VAL GLY GLY ALA LEU GLY
SEQRES 17 A 269 GLU GLU ALA GLY ALA GLN ILE GLN LEU LEU GLU GLU GLY
SEQRES 18 A 269 TRP ASP GLN ARG ALA PRO ILE GLY TRP ASN MET LYS ASP
SEQRES 19 A 269 ALA THR PRO VAL ALA LYS THR VAL CYS ALA LEU LEU SER
SEQRES 20 A 269 ASP TRP LEU PRO ALA THR THR GLY ASP ILE ILE TYR ALA
SEQRES 21 A 269 ASP GLY GLY ALA HIS THR GLN LEU LEU
HET NAD A 301 44
HET ZID A 302 52
HET EPE A 303 15
HET EPE A 304 12
HET DMS A 305 4
HET DMS A 306 4
HET DMS A 307 4
HET DMS A 308 4
HET NA A 309 1
HET NA A 310 1
HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE
HETNAM ZID ISONICOTINIC-ACETYL-NICOTINAMIDE-ADENINE DINUCLEOTIDE
HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HETNAM DMS DIMETHYL SULFOXIDE
HETNAM NA SODIUM ION
HETSYN EPE HEPES
FORMUL 2 NAD C21 H27 N7 O14 P2
FORMUL 3 ZID C27 H30 N8 O15 P2
FORMUL 4 EPE 2(C8 H18 N2 O4 S)
FORMUL 6 DMS 4(C2 H6 O S)
FORMUL 10 NA 2(NA 1+)
FORMUL 12 HOH *266(H2 O)
HELIX 1 AA1 SER A 20 GLN A 32 1 13
HELIX 2 AA2 ARG A 43 ASP A 52 1 10
HELIX 3 AA3 ASN A 67 GLY A 83 1 17
HELIX 4 AA4 PRO A 99 MET A 103 5 5
HELIX 5 AA5 PRO A 107 ALA A 111 5 5
HELIX 6 AA6 PRO A 112 ALA A 124 1 13
HELIX 7 AA7 ALA A 124 LEU A 135 1 12
HELIX 8 AA8 TYR A 158 LYS A 181 1 24
HELIX 9 AA9 THR A 196 GLY A 204 1 9
HELIX 10 AB1 GLY A 208 ALA A 226 1 19
HELIX 11 AB2 ALA A 235 SER A 247 1 13
HELIX 12 AB3 GLY A 263 GLN A 267 5 5
SHEET 1 AA1 7 LEU A 60 GLU A 62 0
SHEET 2 AA1 7 GLN A 35 GLY A 40 1 N LEU A 38 O LEU A 61
SHEET 3 AA1 7 ARG A 9 SER A 13 1 N VAL A 12 O VAL A 37
SHEET 4 AA1 7 LEU A 88 HIS A 93 1 O ASP A 89 N ARG A 9
SHEET 5 AA1 7 MET A 138 ASP A 148 1 O VAL A 145 N HIS A 93
SHEET 6 AA1 7 ARG A 185 ALA A 191 1 O VAL A 189 N ASP A 148
SHEET 7 AA1 7 ASP A 256 ALA A 260 1 O ILE A 258 N LEU A 188
LINK O GLY A 141 NA NA A 310 1555 1555 2.77
LINK O ASP A 223 NA NA A 309 1555 1555 2.50
LINK O GLN A 224 NA NA A 309 1555 1555 2.78
LINK O ALA A 226 NA NA A 309 1555 1555 2.44
LINK OD1 ASP A 248 NA NA A 310 1555 1555 2.45
LINK NA NA A 309 O HOH A 612 1555 1555 2.62
LINK NA NA A 309 O HOH A 627 1555 1555 2.35
LINK NA NA A 309 O HOH A 666 1555 1555 2.21
LINK NA NA A 310 O HOH A 470 1555 1555 2.62
SITE 1 AC1 31 GLY A 14 ILE A 15 ILE A 16 SER A 20
SITE 2 AC1 31 ILE A 21 PHE A 41 LEU A 63 ASP A 64
SITE 3 AC1 31 VAL A 65 SER A 94 ILE A 95 GLY A 96
SITE 4 AC1 31 MET A 147 ASP A 148 LYS A 165 ALA A 191
SITE 5 AC1 31 GLY A 192 PRO A 193 ILE A 194 THR A 196
SITE 6 AC1 31 ZID A 302 HOH A 479 HOH A 490 HOH A 502
SITE 7 AC1 31 HOH A 504 HOH A 528 HOH A 543 HOH A 553
SITE 8 AC1 31 HOH A 576 HOH A 619 HOH A 620
SITE 1 AC2 37 GLY A 14 ILE A 15 ILE A 16 SER A 20
SITE 2 AC2 37 ILE A 21 PHE A 41 LEU A 63 ASP A 64
SITE 3 AC2 37 VAL A 65 SER A 94 ILE A 95 GLY A 96
SITE 4 AC2 37 ILE A 122 MET A 147 ASP A 148 PHE A 149
SITE 5 AC2 37 TYR A 158 LYS A 165 ALA A 191 GLY A 192
SITE 6 AC2 37 PRO A 193 ILE A 194 THR A 196 TRP A 222
SITE 7 AC2 37 NAD A 301 HOH A 479 HOH A 502 HOH A 504
SITE 8 AC2 37 HOH A 528 HOH A 529 HOH A 543 HOH A 553
SITE 9 AC2 37 HOH A 576 HOH A 617 HOH A 619 HOH A 620
SITE 10 AC2 37 HOH A 664
SITE 1 AC3 8 ASP A 42 LEU A 44 ARG A 45 GLU A 62
SITE 2 AC3 8 HIS A 70 HOH A 501 HOH A 511 HOH A 532
SITE 1 AC4 10 SER A 19 HIS A 24 ILE A 194 ARG A 195
SITE 2 AC4 10 THR A 196 LYS A 233 ASP A 234 ALA A 235
SITE 3 AC4 10 HOH A 407 HOH A 411
SITE 1 AC5 3 ILE A 228 GLY A 229 HOH A 571
SITE 1 AC6 5 GLY A 141 GLY A 183 ARG A 185 ILE A 228
SITE 2 AC6 5 PRO A 251
SITE 1 AC7 7 PHE A 109 LYS A 132 PRO A 136 TYR A 182
SITE 2 AC7 7 HOH A 460 HOH A 648 HOH A 660
SITE 1 AC8 4 GLU A 68 ASP A 110 LYS A 132 HOH A 454
SITE 1 AC9 6 ASP A 223 GLN A 224 ALA A 226 HOH A 612
SITE 2 AC9 6 HOH A 627 HOH A 666
SITE 1 AD1 3 GLY A 141 ASP A 248 HOH A 470
CRYST1 97.434 97.434 139.752 90.00 90.00 120.00 P 62 2 2 12
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 0.010263 0.005926 0.000000 0.00000
SCALE2 0.000000 0.011851 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007156 0.00000
(ATOM LINES ARE NOT SHOWN.)
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