HEADER OXIDOREDUCTASE 12-MAY-03 1P9L TITLE STRUCTURE OF M. TUBERCULOSIS DIHYDRODIPICOLINATE REDUCTASE IN COMPLEX TITLE 2 WITH NADH AND 2,6 PDC COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDRODIPICOLINATE REDUCTASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.3.1.26; COMPND 5 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET23A(+) KEYWDS OXIDOREDUCTASE, REDUCTASE, LYSINE BIOSYNTHESIS, NADH BINDING KEYWDS 2 SPECIFICITY, TB STRUCTURAL GENOMICS CONSORTIUM, TBSGC, STRUCTURAL KEYWDS 3 GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE EXPDTA X-RAY DIFFRACTION AUTHOR M.CIRILLI,R.ZHENG,G.SCAPIN,J.S.BLANCHARD,TB STRUCTURAL GENOMICS AUTHOR 2 CONSORTIUM (TBSGC) REVDAT 5 06-NOV-13 1P9L 1 FORMUL HET HETATM HETNAM REVDAT 5 2 1 HETSYN REVDAT 4 13-JUL-11 1P9L 1 VERSN REVDAT 3 24-FEB-09 1P9L 1 VERSN REVDAT 2 30-SEP-03 1P9L 1 JRNL REVDAT 1 26-AUG-03 1P9L 0 JRNL AUTH M.CIRILLI,R.ZHENG,G.SCAPIN,J.S.BLANCHARD JRNL TITL THE THREE-DIMENSIONAL STRUCTURES OF THE MYCOBACTERIUM JRNL TITL 2 TUBERCULOSIS DIHYDRODIPICOLINATE REDUCTASE-NADH-2,6-PDC AND JRNL TITL 3 -NADPH-2,6-PDC COMPLEXES. STRUCTURAL AND MUTAGENIC ANALYSIS JRNL TITL 4 OF RELAXED NUCLEOTIDE SPECIFICITY. JRNL REF BIOCHEMISTRY V. 42 10644 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12962488 JRNL DOI 10.1021/BI030044V REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 0.001 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 10000000.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 24147 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 SET) : 0.193 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.600 REMARK 3 FREE R VALUE TEST SET COUNT : 2379 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2528 REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 273 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 : 3624 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 125 REMARK 3 SOLVENT ATOMS : 117 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.80 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) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.63 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.75 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.900 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.400 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.700 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.600 ; 2.500 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 1P9L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAY-03. REMARK 100 THE RCSB ID CODE IS RCSB019179. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-SEP-96 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SADIE REMARK 200 DATA SCALING SOFTWARE : SAINT REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24502 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07800 REMARK 200 FOR THE DATA SET : 13.6000 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) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.20600 REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1ARZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PEG 400, HEPES, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-Z+1/2 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 59.64500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.27000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.64000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.27000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 59.64500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 58.64000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 59.64500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 58.64000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.27000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.64000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 59.64500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 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 39.27000 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 BIOLOGICAL ASSEMBLY IS A TETRAMER, GENERATED BY A REMARK 300 CRYSTALLOGRAPHIC TWO-FOLD AXIS 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: 18820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 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 238.58000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 58.64000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 GLU A 63 CG CD OE1 OE2 REMARK 470 LYS A 94 CG CD CE NZ 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 227 CD - NE - CZ ANGL. DEV. = 10.1 DEGREES REMARK 500 ARG A 227 NE - CZ - NH1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 227 NE - CZ - NH2 ANGL. DEV. = -7.1 DEGREES REMARK 500 ARG B 227 CD - NE - CZ ANGL. DEV. = 9.5 DEGREES REMARK 500 ARG B 227 NE - CZ - NH1 ANGL. DEV. = -6.4 DEGREES REMARK 500 ARG B 227 NE - CZ - NH2 ANGL. DEV. = 6.4 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 THR A 53 -100.42 -118.28 REMARK 500 SER A 89 -85.43 -57.47 REMARK 500 TRP A 90 -52.60 -21.78 REMARK 500 VAL A 191 -75.22 -116.31 REMARK 500 LEU A 244 -85.10 -135.07 REMARK 500 THR B 53 -99.14 -120.32 REMARK 500 LYS B 94 56.20 -141.11 REMARK 500 VAL B 191 -76.64 -116.59 REMARK 500 GLU B 201 109.68 -50.37 REMARK 500 LEU B 242 2.09 -68.16 REMARK 500 ASP B 243 72.50 44.69 REMARK 500 LEU B 244 -155.96 -176.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 944 DISTANCE = 8.05 ANGSTROMS REMARK 525 HOH A 945 DISTANCE = 7.51 ANGSTROMS REMARK 525 HOH B1439 DISTANCE = 6.76 ANGSTROMS REMARK 525 HOH B1443 DISTANCE = 13.85 ANGSTROMS REMARK 525 HOH B1444 DISTANCE = 10.45 ANGSTROMS REMARK 525 HOH B1456 DISTANCE = 5.09 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAI A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PDC A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAI B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PDC B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 B 2000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ARZ RELATED DB: PDB REMARK 900 ESCHERICHIA COLI DIHYDRODIPICOLINATE REDUCTASE IN COMPLEX REMARK 900 WITH NADH AND 2,6 PYRIDINE DICARBOXYLATE REMARK 900 RELATED ID: 1DIH RELATED DB: PDB REMARK 900 THREE-DIMENSIONAL STRUCTURE OF E. COLI DIHYDRODIPICOLINATE REMARK 900 REDUCTASE REMARK 900 RELATED ID: 1C3V RELATED DB: PDB REMARK 900 DIHYDRODIPICOLINATE REDUCTASE FROM MYCOBACTERIUM REMARK 900 TUBERCULOSIS COMPLEXED WITH NADPH AND PDC REMARK 900 RELATED ID: RV2773C RELATED DB: TARGETDB DBREF 1P9L A 1 245 UNP P72024 DAPB_MYCTU 1 245 DBREF 1P9L B 1 245 UNP P72024 DAPB_MYCTU 1 245 SEQRES 1 A 245 MET ARG VAL GLY VAL LEU GLY ALA LYS GLY LYS VAL GLY SEQRES 2 A 245 THR THR MET VAL ARG ALA VAL ALA ALA ALA ASP ASP LEU SEQRES 3 A 245 THR LEU SER ALA GLU LEU ASP ALA GLY ASP PRO LEU SER SEQRES 4 A 245 LEU LEU THR ASP GLY ASN THR GLU VAL VAL ILE ASP PHE SEQRES 5 A 245 THR HIS PRO ASP VAL VAL MET GLY ASN LEU GLU PHE LEU SEQRES 6 A 245 ILE ASP ASN GLY ILE HIS ALA VAL VAL GLY THR THR GLY SEQRES 7 A 245 PHE THR ALA GLU ARG PHE GLN GLN VAL GLU SER TRP LEU SEQRES 8 A 245 VAL ALA LYS PRO ASN THR SER VAL LEU ILE ALA PRO ASN SEQRES 9 A 245 PHE ALA ILE GLY ALA VAL LEU SER MET HIS PHE ALA LYS SEQRES 10 A 245 GLN ALA ALA ARG PHE PHE ASP SER ALA GLU VAL ILE GLU SEQRES 11 A 245 LEU HIS HIS PRO HIS LYS ALA ASP ALA PRO SER GLY THR SEQRES 12 A 245 ALA ALA ARG THR ALA LYS LEU ILE ALA GLU ALA ARG LYS SEQRES 13 A 245 GLY LEU PRO PRO ASN PRO ASP ALA THR SER THR SER LEU SEQRES 14 A 245 PRO GLY ALA ARG GLY ALA ASP VAL ASP GLY ILE PRO VAL SEQRES 15 A 245 HIS ALA VAL ARG LEU ALA GLY LEU VAL ALA HIS GLN GLU SEQRES 16 A 245 VAL LEU PHE GLY THR GLU GLY GLU THR LEU THR ILE ARG SEQRES 17 A 245 HIS ASP SER LEU ASP ARG THR SER PHE VAL PRO GLY VAL SEQRES 18 A 245 LEU LEU ALA VAL ARG ARG ILE ALA GLU ARG PRO GLY LEU SEQRES 19 A 245 THR VAL GLY LEU GLU PRO LEU LEU ASP LEU HIS SEQRES 1 B 245 MET ARG VAL GLY VAL LEU GLY ALA LYS GLY LYS VAL GLY SEQRES 2 B 245 THR THR MET VAL ARG ALA VAL ALA ALA ALA ASP ASP LEU SEQRES 3 B 245 THR LEU SER ALA GLU LEU ASP ALA GLY ASP PRO LEU SER SEQRES 4 B 245 LEU LEU THR ASP GLY ASN THR GLU VAL VAL ILE ASP PHE SEQRES 5 B 245 THR HIS PRO ASP VAL VAL MET GLY ASN LEU GLU PHE LEU SEQRES 6 B 245 ILE ASP ASN GLY ILE HIS ALA VAL VAL GLY THR THR GLY SEQRES 7 B 245 PHE THR ALA GLU ARG PHE GLN GLN VAL GLU SER TRP LEU SEQRES 8 B 245 VAL ALA LYS PRO ASN THR SER VAL LEU ILE ALA PRO ASN SEQRES 9 B 245 PHE ALA ILE GLY ALA VAL LEU SER MET HIS PHE ALA LYS SEQRES 10 B 245 GLN ALA ALA ARG PHE PHE ASP SER ALA GLU VAL ILE GLU SEQRES 11 B 245 LEU HIS HIS PRO HIS LYS ALA ASP ALA PRO SER GLY THR SEQRES 12 B 245 ALA ALA ARG THR ALA LYS LEU ILE ALA GLU ALA ARG LYS SEQRES 13 B 245 GLY LEU PRO PRO ASN PRO ASP ALA THR SER THR SER LEU SEQRES 14 B 245 PRO GLY ALA ARG GLY ALA ASP VAL ASP GLY ILE PRO VAL SEQRES 15 B 245 HIS ALA VAL ARG LEU ALA GLY LEU VAL ALA HIS GLN GLU SEQRES 16 B 245 VAL LEU PHE GLY THR GLU GLY GLU THR LEU THR ILE ARG SEQRES 17 B 245 HIS ASP SER LEU ASP ARG THR SER PHE VAL PRO GLY VAL SEQRES 18 B 245 LEU LEU ALA VAL ARG ARG ILE ALA GLU ARG PRO GLY LEU SEQRES 19 B 245 THR VAL GLY LEU GLU PRO LEU LEU ASP LEU HIS HET NAI A 301 44 HET PDC A 302 12 HET NAI B 401 44 HET PDC B 402 12 HET PG4 B2000 13 HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE HETNAM PDC PYRIDINE-2,6-DICARBOXYLIC ACID HETNAM PG4 TETRAETHYLENE GLYCOL HETSYN NAI NADH HETSYN PDC DIPICOLINIC ACID FORMUL 3 NAI 2(C21 H29 N7 O14 P2) FORMUL 4 PDC 2(C7 H5 N O4) FORMUL 7 PG4 C8 H18 O5 FORMUL 8 HOH *117(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 ALA A 93 1 14 HELIX 5 5 ALA A 106 ALA A 120 1 15 HELIX 6 6 ARG A 121 PHE A 123 5 3 HELIX 7 7 SER A 141 ARG A 155 1 15 HELIX 8 8 ASP A 213 SER A 216 5 4 HELIX 9 9 PHE A 217 ILE A 228 1 12 HELIX 10 10 ALA A 229 ARG A 231 5 3 HELIX 11 11 LEU A 238 ASP A 243 1 6 HELIX 12 12 GLY B 10 ALA B 23 1 14 HELIX 13 13 LEU B 38 GLY B 44 1 7 HELIX 14 14 VAL B 57 ASN B 68 1 12 HELIX 15 15 THR B 80 ALA B 93 1 14 HELIX 16 16 ALA B 106 ALA B 120 1 15 HELIX 17 17 ARG B 121 PHE B 123 5 3 HELIX 18 18 SER B 141 ARG B 155 1 15 HELIX 19 19 ASP B 213 SER B 216 5 4 HELIX 20 20 PHE B 217 ILE B 228 1 12 HELIX 21 21 ALA B 229 ARG B 231 5 3 SHEET 1 A 6 THR A 27 LEU A 32 0 SHEET 2 A 6 ARG A 2 LEU A 6 1 N VAL A 3 O THR A 27 SHEET 3 A 6 VAL A 48 ASP A 51 1 O ILE A 50 N GLY A 4 SHEET 4 A 6 HIS A 71 VAL A 74 1 O HIS A 71 N VAL A 49 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 GLY A 233 N VAL A 99 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 GLU A 195 N ILE A 129 SHEET 5 B10 GLU A 203 SER A 211 -1 O SER A 211 N ALA A 192 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 ALA B 192 O SER B 211 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 HIS B 183 N VAL B 128 SHEET 10 B10 ALA B 175 VAL B 177 -1 N ALA B 175 O VAL B 182 SHEET 1 C 6 THR B 27 LEU B 32 0 SHEET 2 C 6 ARG B 2 LEU B 6 1 N VAL B 3 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 VAL B 49 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 CISPEP 1 ALA A 139 PRO A 140 0 -0.23 CISPEP 2 ALA B 139 PRO B 140 0 -0.18 SITE 1 AC1 22 GLY A 7 LYS A 9 GLY A 10 LYS A 11 SITE 2 AC1 22 VAL A 12 ASP A 33 ALA A 34 PHE A 52 SITE 3 AC1 22 THR A 53 VAL A 57 GLY A 75 THR A 77 SITE 4 AC1 22 ALA A 102 PRO A 103 ASN A 104 PHE A 105 SITE 5 AC1 22 LYS A 136 PHE A 217 PDC A 302 HOH A 916 SITE 6 AC1 22 HOH A 927 HOH A 935 SITE 1 AC2 10 THR A 77 PRO A 103 ASN A 104 HIS A 133 SITE 2 AC2 10 LYS A 136 SER A 141 GLY A 142 THR A 143 SITE 3 AC2 10 NAI A 301 HOH A 916 SITE 1 AC3 24 LEU B 6 GLY B 7 LYS B 9 GLY B 10 SITE 2 AC3 24 LYS B 11 VAL B 12 ASP B 33 ALA B 34 SITE 3 AC3 24 PHE B 52 THR B 53 VAL B 57 GLY B 75 SITE 4 AC3 24 THR B 76 THR B 77 ALA B 102 PRO B 103 SITE 5 AC3 24 ASN B 104 PHE B 105 LYS B 136 PHE B 217 SITE 6 AC3 24 PDC B 402 HOH B1401 HOH B1420 HOH B1428 SITE 1 AC4 12 THR B 77 PRO B 103 ASN B 104 HIS B 133 SITE 2 AC4 12 LYS B 136 ASP B 138 SER B 141 GLY B 142 SITE 3 AC4 12 THR B 143 NAI B 401 HOH B1420 HOH B1428 SITE 1 AC5 6 THR A 206 ARG A 208 ASP A 210 LEU B 190 SITE 2 AC5 6 ARG B 208 ASP B 210 CRYST1 119.290 117.280 78.540 90.00 90.00 90.00 I 21 21 21 16 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 0.008383 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008527 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012732 0.00000 MASTER 337 0 5 21 22 0 20 6 0 0 0 38 END