PDB Short entry for 1YL5 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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