HEADER OXIDOREDUCTASE 05-OCT-16 5TJY TITLE STRUCTURE OF 4-HYDROXY-TETRAHYDRODIPICOLINATE REDUCTASE FROM TITLE 2 MYCOBACTERIUM TUBERCULOSIS WITH 2,6 PYRIDINE DICARBOXYLIC ACID AND TITLE 3 NADH COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4-HYDROXY-TETRAHYDRODIPICOLINATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HTPA REDUCTASE; COMPND 5 EC: 1.17.1.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25177 / SOURCE 3 H37RA); SOURCE 4 ORGANISM_TAXID: 419947; SOURCE 5 STRAIN: ATCC 25177 / H37RA; SOURCE 6 GENE: DAPB, MRA_2798; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS OXIDOREDUCTASE, LYSINE BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR N.MANK,K.ARNETTE,V.KLAPPER,M.CHRUSZCZ REVDAT 3 04-OCT-23 5TJY 1 REMARK REVDAT 2 30-JUN-21 5TJY 1 JRNL REVDAT 1 18-OCT-17 5TJY 0 JRNL AUTH S.POTE,S.KACHHAP,N.J.MANK,L.DANESHIAN,V.KLAPPER,S.PYE, JRNL AUTH 2 A.K.ARNETTE,L.S.SHIMIZU,T.BOROWSKI,M.CHRUSZCZ JRNL TITL COMPARATIVE STRUCTURAL AND MECHANISTIC STUDIES OF JRNL TITL 2 4-HYDROXY-TETRAHYDRODIPICOLINATE REDUCTASES FROM JRNL TITL 3 MYCOBACTERIUM TUBERCULOSIS AND VIBRIO VULNIFICUS. JRNL REF BIOCHIM BIOPHYS ACTA GEN V.1865 29750 2021 JRNL REF 2 SUBJ JRNL REFN ISSN 1872-8006 JRNL PMID 32980502 JRNL DOI 10.1016/J.BBAGEN.2020.129750 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 12914 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) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 663 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 923 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1807 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 108 REMARK 3 SOLVENT ATOMS : 126 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.99000 REMARK 3 B22 (A**2) : 0.99000 REMARK 3 B33 (A**2) : -3.22000 REMARK 3 B12 (A**2) : 0.50000 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): 0.236 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.190 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.129 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.696 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1964 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1898 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2668 ; 1.914 ; 2.016 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4350 ; 1.012 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 248 ; 6.331 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 74 ;37.123 ;23.514 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 289 ;12.363 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;20.040 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 314 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2189 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 428 ; 0.003 ; 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): 989 ; 3.209 ; 4.063 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 988 ; 3.211 ; 4.058 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1238 ; 4.312 ; 6.080 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5TJY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1000223519. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13744 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 20.50 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.70 REMARK 200 R MERGE FOR SHELL (I) : 0.81300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: 1C3V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM AMMONIUM SULFATE, 50 MM BIS-TRIS REMARK 280 PH 6.5, 30% V/V PENTAERYTHRITOL ETHOXYLATE (15/4 EO/OH), VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 166.24200 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 83.12100 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 166.24200 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 83.12100 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 166.24200 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 83.12100 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 166.24200 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 83.12100 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 24420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -199.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 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 C BEZ A 304 LIES ON A SPECIAL POSITION. REMARK 375 C1 BEZ A 304 LIES ON A SPECIAL POSITION. REMARK 375 C4 BEZ A 304 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 523 LIES ON A SPECIAL POSITION. 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 83 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 83 NE - CZ - NH1 ANGL. DEV. = 3.7 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 30 148.41 -174.33 REMARK 500 ASP A 33 -165.78 -126.85 REMARK 500 THR A 53 -108.62 -118.50 REMARK 500 ASP A 163 114.56 -163.37 REMARK 500 VAL A 191 -93.42 -116.01 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 PG4 A 306 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 307 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 20 O REMARK 620 2 ALA A 21 O 77.6 REMARK 620 3 ALA A 23 O 92.4 93.5 REMARK 620 4 LEU A 26 O 95.6 172.6 89.6 REMARK 620 5 HOH A 482 O 100.5 85.3 166.4 93.2 REMARK 620 6 HOH A 491 O 153.6 87.1 110.1 98.2 56.3 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 PDC A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAI A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BEZ A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IMD A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 313 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 314 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TJZ RELATED DB: PDB DBREF 5TJY A 1 244 UNP A5U6C6 DAPB_MYCTA 1 244 SEQADV 5TJY GLY A 0 UNP A5U6C6 EXPRESSION TAG SEQRES 1 A 245 GLY MET ARG VAL GLY VAL LEU GLY ALA LYS GLY LYS VAL SEQRES 2 A 245 GLY ALA THR MET VAL ARG ALA VAL ALA ALA ALA ASP ASP SEQRES 3 A 245 LEU THR LEU SER ALA GLU LEU ASP ALA GLY ASP PRO LEU SEQRES 4 A 245 SER LEU LEU THR ASP GLY ASN THR GLU VAL VAL ILE ASP SEQRES 5 A 245 PHE THR HIS PRO ASP VAL VAL MET GLY ASN LEU GLU PHE SEQRES 6 A 245 LEU ILE ASP ASN GLY ILE HIS ALA VAL VAL GLY THR THR SEQRES 7 A 245 GLY PHE THR ALA GLU ARG PHE GLN GLN VAL GLU SER TRP SEQRES 8 A 245 LEU VAL ALA LYS PRO ASN THR SER VAL LEU ILE ALA PRO SEQRES 9 A 245 ASN PHE ALA ILE GLY ALA VAL LEU SER MET HIS PHE ALA SEQRES 10 A 245 LYS GLN ALA ALA ARG PHE PHE ASP SER ALA GLU VAL ILE SEQRES 11 A 245 GLU LEU HIS HIS PRO HIS LYS ALA ASP ALA PRO SER GLY SEQRES 12 A 245 THR ALA ALA ARG THR ALA LYS LEU ILE ALA GLU ALA ARG SEQRES 13 A 245 LYS GLY LEU PRO PRO ASN PRO ASP ALA THR SER THR SER SEQRES 14 A 245 LEU PRO GLY ALA ARG GLY ALA ASP VAL ASP GLY ILE PRO SEQRES 15 A 245 VAL HIS ALA VAL ARG LEU ALA GLY LEU VAL ALA HIS GLN SEQRES 16 A 245 GLU VAL LEU PHE GLY THR GLU GLY GLU THR LEU THR ILE SEQRES 17 A 245 ARG HIS ASP SER LEU ASP ARG THR SER PHE VAL PRO GLY SEQRES 18 A 245 VAL LEU LEU ALA VAL ARG ARG ILE ALA GLU ARG PRO GLY SEQRES 19 A 245 LEU THR VAL GLY LEU GLU PRO LEU LEU ASP LEU HET PDC A 301 12 HET NAI A 302 44 HET SO4 A 303 5 HET BEZ A 304 9 HET IMD A 305 5 HET PG4 A 306 7 HET NA A 307 1 HET EDO A 308 4 HET EDO A 309 4 HET EDO A 310 4 HET EDO A 311 4 HET EDO A 312 4 HET EDO A 313 4 HET CL A 314 1 HETNAM PDC PYRIDINE-2,6-DICARBOXYLIC ACID HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE HETNAM SO4 SULFATE ION HETNAM BEZ BENZOIC ACID HETNAM IMD IMIDAZOLE HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM NA SODIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETSYN PDC DIPICOLINIC ACID HETSYN NAI NADH HETSYN EDO ETHYLENE GLYCOL FORMUL 2 PDC C7 H5 N O4 FORMUL 3 NAI C21 H29 N7 O14 P2 FORMUL 4 SO4 O4 S 2- FORMUL 5 BEZ C7 H6 O2 FORMUL 6 IMD C3 H5 N2 1+ FORMUL 7 PG4 C8 H18 O5 FORMUL 8 NA NA 1+ FORMUL 9 EDO 6(C2 H6 O2) FORMUL 15 CL CL 1- FORMUL 16 HOH *126(H2 O) HELIX 1 AA1 GLY A 10 ALA A 23 1 14 HELIX 2 AA2 LEU A 38 GLY A 44 1 7 HELIX 3 AA3 VAL A 57 ASN A 68 1 12 HELIX 4 AA4 THR A 80 ALA A 93 1 14 HELIX 5 AA5 ALA A 106 ALA A 120 1 15 HELIX 6 AA6 ARG A 121 PHE A 123 5 3 HELIX 7 AA7 SER A 141 ARG A 155 1 15 HELIX 8 AA8 ASP A 213 SER A 216 5 4 HELIX 9 AA9 PHE A 217 ILE A 228 1 12 HELIX 10 AB1 ALA A 229 ARG A 231 5 3 HELIX 11 AB2 LEU A 238 LEU A 242 5 5 SHEET 1 AA1 6 LEU A 26 LEU A 32 0 SHEET 2 AA1 6 MET A 1 LEU A 6 1 N MET A 1 O THR A 27 SHEET 3 AA1 6 VAL A 48 ASP A 51 1 O ILE A 50 N LEU A 6 SHEET 4 AA1 6 HIS A 71 VAL A 74 1 O VAL A 73 N VAL A 49 SHEET 5 AA1 6 SER A 98 ILE A 101 1 O LEU A 100 N VAL A 74 SHEET 6 AA1 6 GLY A 233 VAL A 236 1 O GLY A 233 N VAL A 99 SHEET 1 AA2 5 ALA A 175 VAL A 177 0 SHEET 2 AA2 5 ILE A 180 ARG A 186 -1 O VAL A 182 N ALA A 175 SHEET 3 AA2 5 SER A 125 HIS A 132 1 N GLU A 130 O VAL A 185 SHEET 4 AA2 5 ALA A 192 THR A 200 -1 O HIS A 193 N LEU A 131 SHEET 5 AA2 5 GLU A 203 SER A 211 -1 O SER A 211 N ALA A 192 LINK O VAL A 20 NA NA A 307 1555 1555 2.47 LINK O ALA A 21 NA NA A 307 1555 1555 2.47 LINK O ALA A 23 NA NA A 307 1555 1555 2.38 LINK O LEU A 26 NA NA A 307 1555 1555 2.11 LINK NA NA A 307 O HOH A 482 1555 1555 3.10 LINK NA NA A 307 O HOH A 491 1555 1555 2.31 CISPEP 1 ALA A 139 PRO A 140 0 -5.78 SITE 1 AC1 12 THR A 77 PRO A 103 ASN A 104 HIS A 133 SITE 2 AC1 12 LYS A 136 SER A 141 GLY A 142 THR A 143 SITE 3 AC1 12 ALA A 192 NAI A 302 HOH A 413 HOH A 420 SITE 1 AC2 26 GLY A 7 LYS A 9 GLY A 10 LYS A 11 SITE 2 AC2 26 VAL A 12 ASP A 33 ALA A 34 PHE A 52 SITE 3 AC2 26 THR A 53 VAL A 57 GLY A 75 THR A 76 SITE 4 AC2 26 THR A 77 ALA A 102 PRO A 103 ASN A 104 SITE 5 AC2 26 PHE A 105 LYS A 136 ASP A 138 PHE A 217 SITE 6 AC2 26 PDC A 301 HOH A 404 HOH A 410 HOH A 413 SITE 7 AC2 26 HOH A 420 HOH A 429 SITE 1 AC3 4 GLY A 78 ALA A 139 PRO A 140 HOH A 401 SITE 1 AC4 4 MET A 59 ARG A 83 IMD A 305 HOH A 418 SITE 1 AC5 5 MET A 59 GLY A 60 GLU A 63 TRP A 90 SITE 2 AC5 5 BEZ A 304 SITE 1 AC6 4 GLU A 195 THR A 206 ARG A 208 ASP A 210 SITE 1 AC7 5 VAL A 20 ALA A 21 ALA A 23 LEU A 26 SITE 2 AC7 5 HOH A 491 SITE 1 AC8 1 PHE A 122 SITE 1 AC9 1 ASN A 45 SITE 1 AD1 4 ARG A 173 GLY A 174 ASP A 176 PRO A 181 SITE 1 AD2 3 ASP A 176 ASP A 178 GLY A 179 SITE 1 AD3 2 ASN A 161 ASP A 163 SITE 1 AD4 4 GLY A 237 LEU A 238 GLU A 239 HOH A 433 CRYST1 66.421 66.421 249.363 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 0.015055 0.008692 0.000000 0.00000 SCALE2 0.000000 0.017385 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004010 0.00000