HEADER OXIDOREDUCTASE 19-JAN-05 1YL5 TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DIHYDRODIPICOLINATE TITLE 2 REDUCTASE (RV2773C) (CRYSTAL FORM A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDRODIPICOLINATE REDUCTASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DHPR; COMPND 5 EC: 1.3.1.26; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: DAPB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RP; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETM-11 KEYWDS LYSINE BIOSYNTHESIS, DIHYDRODIPICOLINATE, REDUCTASE, NADH, STRUCTURAL KEYWDS 2 GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, TB STRUCTURAL GENOMICS KEYWDS 3 CONSORTIUM, TBSGC, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR R.JANOWSKI,G.KEFALA,M.S.WEISS,TB STRUCTURAL GENOMICS CONSORTIUM AUTHOR 2 (TBSGC) REVDAT 6 23-AUG-23 1YL5 1 REMARK SEQADV LINK REVDAT 5 11-OCT-17 1YL5 1 REMARK REVDAT 4 13-JUL-11 1YL5 1 VERSN REVDAT 3 26-JAN-10 1YL5 1 JRNL REVDAT 2 24-FEB-09 1YL5 1 VERSN REVDAT 1 17-JAN-06 1YL5 0 JRNL AUTH R.JANOWSKI,G.KEFALA,M.S.WEISS JRNL TITL THE STRUCTURE OF DIHYDRODIPICOLINATE REDUCTASE (DAPB) FROM JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS IN THREE CRYSTAL FORMS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 66 61 2010 JRNL REFN ISSN 0907-4449 JRNL PMID 20057050 JRNL DOI 10.1107/S0907444909043960 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 24648 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1056 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.42 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3489 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 146 REMARK 3 BIN FREE R VALUE : 0.3480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3648 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 49 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 42.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.79000 REMARK 3 B22 (A**2) : -3.04000 REMARK 3 B33 (A**2) : -0.75000 REMARK 3 B12 (A**2) : 0.00000 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): 0.294 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.225 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.186 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.266 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3718 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5072 ; 1.529 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 492 ; 5.941 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 146 ;35.483 ;23.562 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 572 ;16.758 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;22.779 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 612 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2810 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1789 ; 0.224 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2538 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 193 ; 0.149 ; 0.200 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): 104 ; 0.231 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.178 ; 0.200 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): 2503 ; 0.854 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3938 ; 1.547 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1304 ; 3.924 ; 5.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1134 ; 6.212 ;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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 105 REMARK 3 RESIDUE RANGE : A 218 A 245 REMARK 3 ORIGIN FOR THE GROUP (A): 11.6592 39.9977 -3.7690 REMARK 3 T TENSOR REMARK 3 T11: -0.1342 T22: -0.1005 REMARK 3 T33: -0.1750 T12: -0.1240 REMARK 3 T13: 0.0578 T23: -0.0198 REMARK 3 L TENSOR REMARK 3 L11: 5.0893 L22: 3.8877 REMARK 3 L33: 8.1178 L12: 1.2821 REMARK 3 L13: 1.4273 L23: 0.5375 REMARK 3 S TENSOR REMARK 3 S11: 0.1218 S12: 0.0260 S13: 0.1285 REMARK 3 S21: 0.5408 S22: -0.2567 S23: 0.3221 REMARK 3 S31: -0.1507 S32: -0.3143 S33: 0.1349 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 106 A 217 REMARK 3 ORIGIN FOR THE GROUP (A): 15.9724 57.1343 19.1921 REMARK 3 T TENSOR REMARK 3 T11: -0.0487 T22: -0.0530 REMARK 3 T33: -0.0197 T12: -0.0221 REMARK 3 T13: -0.0590 T23: -0.0045 REMARK 3 L TENSOR REMARK 3 L11: 1.3013 L22: 3.3239 REMARK 3 L33: 0.0455 L12: 0.4440 REMARK 3 L13: 0.2093 L23: -0.1224 REMARK 3 S TENSOR REMARK 3 S11: -0.0387 S12: 0.0028 S13: 0.0732 REMARK 3 S21: -0.3603 S22: 0.0024 S23: 0.4305 REMARK 3 S31: 0.1720 S32: -0.3062 S33: 0.0363 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 0 B 105 REMARK 3 RESIDUE RANGE : B 218 B 245 REMARK 3 ORIGIN FOR THE GROUP (A): 25.6580 33.8394 44.8830 REMARK 3 T TENSOR REMARK 3 T11: -0.2634 T22: 0.0134 REMARK 3 T33: -0.0547 T12: -0.0408 REMARK 3 T13: -0.0190 T23: 0.0088 REMARK 3 L TENSOR REMARK 3 L11: 1.5829 L22: 3.8975 REMARK 3 L33: 4.5313 L12: -0.4116 REMARK 3 L13: -0.3067 L23: 0.4156 REMARK 3 S TENSOR REMARK 3 S11: -0.1020 S12: -0.1889 S13: -0.0110 REMARK 3 S21: 0.0150 S22: 0.0320 S23: -0.1305 REMARK 3 S31: -0.0968 S32: 0.1546 S33: 0.0700 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 106 B 217 REMARK 3 ORIGIN FOR THE GROUP (A): 35.9665 48.4535 21.9664 REMARK 3 T TENSOR REMARK 3 T11: -0.0236 T22: -0.1482 REMARK 3 T33: 0.0077 T12: 0.0228 REMARK 3 T13: 0.0065 T23: 0.0152 REMARK 3 L TENSOR REMARK 3 L11: 2.4474 L22: 1.8315 REMARK 3 L33: 1.6434 L12: 1.2097 REMARK 3 L13: 0.0838 L23: -0.2026 REMARK 3 S TENSOR REMARK 3 S11: 0.0265 S12: -0.1047 S13: -0.4711 REMARK 3 S21: -0.1510 S22: -0.1123 S23: -0.3952 REMARK 3 S31: 0.3081 S32: 0.0966 S33: 0.0858 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: TLS REFINEMENT REMARK 4 REMARK 4 1YL5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000031641. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.10 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL (SI111, SI220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25757 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 63.10 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.73300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.750 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 1P9L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS/HCL, 20 % PEG 3350, 120 MM REMARK 280 MGCL2 , PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 29.63000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 61.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.63000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 61.00000 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 SECOND PART OF THE BIOLOGICAL ASSEMBLY (TETRAMER) IS REMARK 300 GENERATED BY THE TWO FOLD AXIS: 1/2, 1/2, Z. 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 12150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -104.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 59.26000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 122.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 LEU A 131 CA - CB - CG ANGL. DEV. = 14.5 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 ALA A 34 103.32 -24.92 REMARK 500 THR A 53 -150.80 -84.40 REMARK 500 VAL A 191 -89.31 -114.03 REMARK 500 ALA B 30 134.01 -170.15 REMARK 500 ALA B 34 114.18 -22.95 REMARK 500 THR B 77 -165.61 -100.21 REMARK 500 ASP B 163 109.99 -166.09 REMARK 500 VAL B 191 -89.50 -121.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 246 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 20 O REMARK 620 2 ALA A 21 O 79.3 REMARK 620 3 ALA A 23 O 91.6 101.0 REMARK 620 4 LEU A 26 O 94.8 173.7 76.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 246 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL B 20 O REMARK 620 2 ALA B 21 O 76.4 REMARK 620 3 ALA B 23 O 101.4 89.2 REMARK 620 4 LEU B 26 O 99.7 172.6 97.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 246 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 246 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YL6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DIHYDRODIPICOLINATE REMARK 900 REDUCTASE (RV2773C) (CRYSTAL FORM B) REMARK 900 RELATED ID: 1YL7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DIHYDRODIPICOLINATE REMARK 900 REDUCTASE (RV2773C) IN COMPLEX WITH NADH (CRYSTAL FORM C) REMARK 900 RELATED ID: RV2773C RELATED DB: TARGETDB DBREF 1YL5 A 2 245 UNP P72024 DAPB_MYCTU 2 245 DBREF 1YL5 B 2 245 UNP P72024 DAPB_MYCTU 2 245 SEQADV 1YL5 ALA A 0 UNP P72024 CLONING ARTIFACT SEQADV 1YL5 MET A 1 UNP P72024 CLONING ARTIFACT SEQADV 1YL5 ALA A 0 UNP P72024 CLONING ARTIFACT SEQADV 1YL5 ALA B 0 UNP P72024 CLONING ARTIFACT SEQADV 1YL5 MET B 1 UNP P72024 CLONING ARTIFACT SEQADV 1YL5 ALA B 0 UNP P72024 CLONING ARTIFACT SEQRES 1 A 247 ALA MET ALA ARG VAL GLY VAL LEU GLY ALA LYS GLY LYS SEQRES 2 A 247 VAL GLY ALA THR MET VAL ARG ALA VAL ALA ALA ALA ASP SEQRES 3 A 247 ASP LEU THR LEU SER ALA GLU LEU ASP ALA GLY ASP PRO SEQRES 4 A 247 LEU SER LEU LEU THR ASP GLY ASN THR GLU VAL VAL ILE SEQRES 5 A 247 ASP PHE THR HIS PRO ASP VAL VAL MET GLY ASN LEU GLU SEQRES 6 A 247 PHE LEU ILE ASP ASN GLY ILE HIS ALA VAL VAL GLY THR SEQRES 7 A 247 THR GLY PHE THR ALA GLU ARG PHE GLN GLN VAL GLU SER SEQRES 8 A 247 TRP LEU VAL ALA LYS PRO ASN THR SER VAL LEU ILE ALA SEQRES 9 A 247 PRO ASN PHE ALA ILE GLY ALA VAL LEU SER MET HIS PHE SEQRES 10 A 247 ALA LYS GLN ALA ALA ARG PHE PHE ASP SER ALA GLU VAL SEQRES 11 A 247 ILE GLU LEU HIS HIS PRO HIS LYS ALA ASP ALA PRO SER SEQRES 12 A 247 GLY THR ALA ALA ARG THR ALA LYS LEU ILE ALA GLU ALA SEQRES 13 A 247 ARG LYS GLY LEU PRO PRO ASN PRO ASP ALA THR SER THR SEQRES 14 A 247 SER LEU PRO GLY ALA ARG GLY ALA ASP VAL ASP GLY ILE SEQRES 15 A 247 PRO VAL HIS ALA VAL ARG LEU ALA GLY LEU VAL ALA HIS SEQRES 16 A 247 GLN GLU VAL LEU PHE GLY THR GLU GLY GLU THR LEU THR SEQRES 17 A 247 ILE ARG HIS ASP SER LEU ASP ARG THR SER PHE VAL PRO SEQRES 18 A 247 GLY VAL LEU LEU ALA VAL ARG ARG ILE ALA GLU ARG PRO SEQRES 19 A 247 GLY LEU THR VAL GLY LEU GLU PRO LEU LEU ASP LEU HIS SEQRES 1 B 247 ALA MET ALA ARG VAL GLY VAL LEU GLY ALA LYS GLY LYS SEQRES 2 B 247 VAL GLY ALA THR MET VAL ARG ALA VAL ALA ALA ALA ASP SEQRES 3 B 247 ASP LEU THR LEU SER ALA GLU LEU ASP ALA GLY ASP PRO SEQRES 4 B 247 LEU SER LEU LEU THR ASP GLY ASN THR GLU VAL VAL ILE SEQRES 5 B 247 ASP PHE THR HIS PRO ASP VAL VAL MET GLY ASN LEU GLU SEQRES 6 B 247 PHE LEU ILE ASP ASN GLY ILE HIS ALA VAL VAL GLY THR SEQRES 7 B 247 THR GLY PHE THR ALA GLU ARG PHE GLN GLN VAL GLU SER SEQRES 8 B 247 TRP LEU VAL ALA LYS PRO ASN THR SER VAL LEU ILE ALA SEQRES 9 B 247 PRO ASN PHE ALA ILE GLY ALA VAL LEU SER MET HIS PHE SEQRES 10 B 247 ALA LYS GLN ALA ALA ARG PHE PHE ASP SER ALA GLU VAL SEQRES 11 B 247 ILE GLU LEU HIS HIS PRO HIS LYS ALA ASP ALA PRO SER SEQRES 12 B 247 GLY THR ALA ALA ARG THR ALA LYS LEU ILE ALA GLU ALA SEQRES 13 B 247 ARG LYS GLY LEU PRO PRO ASN PRO ASP ALA THR SER THR SEQRES 14 B 247 SER LEU PRO GLY ALA ARG GLY ALA ASP VAL ASP GLY ILE SEQRES 15 B 247 PRO VAL HIS ALA VAL ARG LEU ALA GLY LEU VAL ALA HIS SEQRES 16 B 247 GLN GLU VAL LEU PHE GLY THR GLU GLY GLU THR LEU THR SEQRES 17 B 247 ILE ARG HIS ASP SER LEU ASP ARG THR SER PHE VAL PRO SEQRES 18 B 247 GLY VAL LEU LEU ALA VAL ARG ARG ILE ALA GLU ARG PRO SEQRES 19 B 247 GLY LEU THR VAL GLY LEU GLU PRO LEU LEU ASP LEU HIS HET MG A 246 1 HET MG B 246 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *49(H2 O) HELIX 1 1 GLY A 10 ALA A 23 1 14 HELIX 2 2 LEU A 38 GLY A 44 1 7 HELIX 3 3 VAL A 57 ASN A 68 1 12 HELIX 4 4 THR A 80 LYS A 94 1 15 HELIX 5 5 ALA A 106 ARG A 121 1 16 HELIX 6 6 SER A 141 ARG A 155 1 15 HELIX 7 7 PHE A 217 ILE A 228 1 12 HELIX 8 8 ALA A 229 ARG A 231 5 3 HELIX 9 9 LEU A 238 ASP A 243 5 6 HELIX 10 10 GLY B 10 ALA B 23 1 14 HELIX 11 11 LEU B 38 GLY B 44 1 7 HELIX 12 12 HIS B 54 ASN B 68 1 15 HELIX 13 13 THR B 80 ALA B 93 1 14 HELIX 14 14 ALA B 106 ARG B 121 1 16 HELIX 15 15 SER B 141 ARG B 155 1 15 HELIX 16 16 PHE B 217 ILE B 228 1 12 HELIX 17 17 ALA B 229 ARG B 231 5 3 HELIX 18 18 LEU B 238 ASP B 243 5 6 SHEET 1 A 6 LEU A 26 LEU A 32 0 SHEET 2 A 6 ALA A 1A LEU A 6 1 N VAL A 3 O THR A 27 SHEET 3 A 6 VAL A 48 ASP A 51 1 O VAL A 48 N GLY A 4 SHEET 4 A 6 HIS A 71 VAL A 74 1 O VAL A 73 N ASP A 51 SHEET 5 A 6 SER A 98 ILE A 101 1 O LEU A 100 N VAL A 74 SHEET 6 A 6 GLY A 233 VAL A 236 1 O THR A 235 N ILE A 101 SHEET 1 B10 ALA A 175 VAL A 177 0 SHEET 2 B10 ILE A 180 ARG A 186 -1 O VAL A 182 N ALA A 175 SHEET 3 B10 SER A 125 HIS A 132 1 N GLU A 130 O VAL A 185 SHEET 4 B10 ALA A 192 THR A 200 -1 O HIS A 193 N LEU A 131 SHEET 5 B10 GLU A 203 SER A 211 -1 O HIS A 209 N GLN A 194 SHEET 6 B10 GLU B 203 SER B 211 -1 O ARG B 208 N THR A 206 SHEET 7 B10 ALA B 192 THR B 200 -1 N GLN B 194 O HIS B 209 SHEET 8 B10 SER B 125 HIS B 132 -1 N ILE B 129 O GLU B 195 SHEET 9 B10 ILE B 180 ARG B 186 1 O VAL B 185 N GLU B 130 SHEET 10 B10 ALA B 175 VAL B 177 -1 N ALA B 175 O VAL B 182 SHEET 1 C 6 LEU B 26 GLU B 31 0 SHEET 2 C 6 ALA B 1A LEU B 6 1 N ALA B 1A O THR B 27 SHEET 3 C 6 VAL B 48 ASP B 51 1 O ILE B 50 N LEU B 6 SHEET 4 C 6 HIS B 71 VAL B 74 1 O VAL B 73 N ASP B 51 SHEET 5 C 6 SER B 98 ILE B 101 1 O LEU B 100 N VAL B 74 SHEET 6 C 6 GLY B 233 VAL B 236 1 O THR B 235 N VAL B 99 LINK O VAL A 20 MG MG A 246 1555 1555 2.35 LINK O ALA A 21 MG MG A 246 1555 1555 2.58 LINK O ALA A 23 MG MG A 246 1555 1555 2.40 LINK O LEU A 26 MG MG A 246 1555 1555 2.30 LINK O VAL B 20 MG MG B 246 1555 1555 2.24 LINK O ALA B 21 MG MG B 246 1555 1555 2.73 LINK O ALA B 23 MG MG B 246 1555 1555 2.30 LINK O LEU B 26 MG MG B 246 1555 1555 2.28 CISPEP 1 ALA A 139 PRO A 140 0 -0.49 CISPEP 2 ALA B 139 PRO B 140 0 -2.02 SITE 1 AC1 4 VAL A 20 ALA A 21 ALA A 23 LEU A 26 SITE 1 AC2 4 VAL B 20 ALA B 21 ALA B 23 LEU B 26 CRYST1 59.260 122.000 77.930 90.00 90.00 90.00 P 21 21 2 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 0.016875 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008197 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012832 0.00000 CONECT 144 3651 CONECT 151 3651 CONECT 161 3651 CONECT 182 3651 CONECT 1969 3652 CONECT 1976 3652 CONECT 1986 3652 CONECT 2007 3652 CONECT 3651 144 151 161 182 CONECT 3652 1969 1976 1986 2007 MASTER 402 0 2 18 22 0 2 6 3699 2 10 38 END