HEADER LIGASE 10-AUG-09 3IME TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE TITLE 2 SYNTHETASE AT 2.40 ANG RESOLUTION IN COMPLEX WITH FRAGMENT COMPOUND TITLE 3 1-BENZOFURAN-2-CARBOXYLIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: PANTOTHENATE SYNTHETASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-300; COMPND 5 SYNONYM: PS, PANTOATE-BETA-ALANINE LIGASE, PANTOATE-ACTIVATING COMPND 6 ENZYME; COMPND 7 EC: 6.3.2.1; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: MT3707, MTCY07H7B.20, PANC, RV3602C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: C41(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS MYCOBACTERIUM TUBERCULOSIS, PANTOTHENATE BIOSYNTHESIS, ENZYMES, KEYWDS 2 LIGASE, DRUG DESIGN, FRAGMENT-BASED, ATP-BINDING, MAGNESIUM, METAL- KEYWDS 3 BINDING, NUCLEOTIDE-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.CIULLI,A.W.HUNG,H.L.SILVESTRE,S.WEN,T.L.BLUNDELL,C.ABELL REVDAT 6 06-SEP-23 3IME 1 REMARK REVDAT 5 13-OCT-21 3IME 1 REMARK SEQADV REVDAT 4 13-JUL-11 3IME 1 VERSN REVDAT 3 02-MAR-11 3IME 1 HETSYN REVDAT 2 10-NOV-09 3IME 1 JRNL REVDAT 1 13-OCT-09 3IME 0 JRNL AUTH A.W.HUNG,H.L.SILVESTRE,S.WEN,A.CIULLI,T.L.BLUNDELL,C.ABELL JRNL TITL APPLICATION OF FRAGMENT GROWING AND FRAGMENT LINKING TO THE JRNL TITL 2 DISCOVERY OF INHIBITORS OF MYCOBACTERIUM TUBERCULOSIS JRNL TITL 3 PANTOTHENATE SYNTHETASE. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 48 8452 2009 JRNL REFN ISSN 1433-7851 JRNL PMID 19780086 JRNL DOI 10.1002/ANIE.200903821 REMARK 2 REMARK 2 RESOLUTION. 2.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 20730 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1120 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) : 2.39 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.45 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1415 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.1830 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4084 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 248 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.443 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.293 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.202 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.610 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.896 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4194 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5720 ; 1.773 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 551 ; 6.879 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 164 ;37.040 ;22.561 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 624 ;16.867 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 43 ;14.617 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 686 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3188 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1850 ; 0.220 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2833 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 241 ; 0.175 ; 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): 54 ; 0.196 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.174 ; 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): 2825 ; 3.834 ; 5.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4412 ; 5.198 ; 6.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1501 ; 4.935 ; 5.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1308 ; 6.794 ; 7.500 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 : 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 3IME COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054592. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX10.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.117 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21873 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.390 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : 0.12700 REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.45800 REMARK 200 R SYM FOR SHELL (I) : 0.45800 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 3COV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 11-14% W/V PEG3000, 100-150 MM LITHIUM REMARK 280 SULFATE, 100 MM IMIDAZOLE, PH 8.0, 2-4% V/V ETHANOL, 10% V/V REMARK 280 GLYCEROL AND 20 MM MAGNESIUM CHLORIDE. , VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 35.66900 REMARK 290 SMTRY3 2 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 ALA A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ILE A 3 REMARK 465 PRO A 259 REMARK 465 MET A 260 REMARK 465 PRO A 261 REMARK 465 LEU A 262 REMARK 465 PHE A 290 REMARK 465 ALA A 291 REMARK 465 GLY A 292 REMARK 465 THR A 293 REMARK 465 ASP A 294 REMARK 465 ARG A 295 REMARK 465 PRO A 296 REMARK 465 ASP A 297 REMARK 465 GLY A 298 REMARK 465 TYR A 299 REMARK 465 ARG A 300 REMARK 465 ALA B 0 REMARK 465 MET B 1 REMARK 465 MET B 71 REMARK 465 GLN B 72 REMARK 465 PHE B 73 REMARK 465 GLY B 74 REMARK 465 ALA B 75 REMARK 465 GLY B 76 REMARK 465 GLY B 77 REMARK 465 ASP B 78 REMARK 465 LEU B 79 REMARK 465 ASP B 80 REMARK 465 ALA B 81 REMARK 465 TYR B 82 REMARK 465 PRO B 83 REMARK 465 ARG B 84 REMARK 465 THR B 289 REMARK 465 PHE B 290 REMARK 465 ALA B 291 REMARK 465 GLY B 292 REMARK 465 THR B 293 REMARK 465 ASP B 294 REMARK 465 ARG B 295 REMARK 465 PRO B 296 REMARK 465 ASP B 297 REMARK 465 GLY B 298 REMARK 465 TYR B 299 REMARK 465 ARG B 300 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH1 ARG A 56 O HOH A 366 2.08 REMARK 500 OG1 THR A 186 O HOH A 687 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 VAL B 142 CB VAL B 142 CG2 -0.133 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 PRO B 122 C - N - CA ANGL. DEV. = 10.6 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 85 56.43 -143.93 REMARK 500 ASP A 87 -71.75 -45.00 REMARK 500 ARG A 115 -93.56 -115.43 REMARK 500 LEU A 127 -109.39 56.75 REMARK 500 ARG A 132 66.97 -119.33 REMARK 500 ARG A 151 59.38 38.68 REMARK 500 LEU A 257 25.37 81.77 REMARK 500 ARG B 115 -92.03 -120.02 REMARK 500 LEU B 127 -96.17 55.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU B 128 GLY B 129 64.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BZ2 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EOH A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EOH A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BZ2 B 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3COV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE REMARK 900 SYNTHETASE AT 1.5 ANG RESOLUTION- APO FORM REMARK 900 RELATED ID: 3IMC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE REMARK 900 SYNTHETASE AT 1.60 ANG RESOLUTION IN COMPLEX WITH FRAGMENT COMPOUND REMARK 900 5-METHOXYINDOLE, SULFATE AND GLYCEROL REMARK 900 RELATED ID: 3IMG RELATED DB: PDB REMARK 900 SAME PROTEIN AT 1.8 ANG RESOLUTION IN A TERNARY COMPLEX WITH REMARK 900 FRAGMENT COMPOUNDS 5-METHOXYINDOLE AND 1-BENZOFURAN-2-CARBOXYLIC REMARK 900 ACID DBREF 3IME A 1 300 UNP P0A5R0 PANC_MYCTU 1 300 DBREF 3IME B 1 300 UNP P0A5R0 PANC_MYCTU 1 300 SEQADV 3IME ALA A 0 UNP P0A5R0 EXPRESSION TAG SEQADV 3IME ALA A 2 UNP P0A5R0 THR 2 ENGINEERED MUTATION SEQADV 3IME GLY A 77 UNP P0A5R0 GLU 77 ENGINEERED MUTATION SEQADV 3IME ALA B 0 UNP P0A5R0 EXPRESSION TAG SEQADV 3IME ALA B 2 UNP P0A5R0 THR 2 ENGINEERED MUTATION SEQADV 3IME GLY B 77 UNP P0A5R0 GLU 77 ENGINEERED MUTATION SEQRES 1 A 301 ALA MET ALA ILE PRO ALA PHE HIS PRO GLY GLU LEU ASN SEQRES 2 A 301 VAL TYR SER ALA PRO GLY ASP VAL ALA ASP VAL SER ARG SEQRES 3 A 301 ALA LEU ARG LEU THR GLY ARG ARG VAL MET LEU VAL PRO SEQRES 4 A 301 THR MET GLY ALA LEU HIS GLU GLY HIS LEU ALA LEU VAL SEQRES 5 A 301 ARG ALA ALA LYS ARG VAL PRO GLY SER VAL VAL VAL VAL SEQRES 6 A 301 SER ILE PHE VAL ASN PRO MET GLN PHE GLY ALA GLY GLY SEQRES 7 A 301 ASP LEU ASP ALA TYR PRO ARG THR PRO ASP ASP ASP LEU SEQRES 8 A 301 ALA GLN LEU ARG ALA GLU GLY VAL GLU ILE ALA PHE THR SEQRES 9 A 301 PRO THR THR ALA ALA MET TYR PRO ASP GLY LEU ARG THR SEQRES 10 A 301 THR VAL GLN PRO GLY PRO LEU ALA ALA GLU LEU GLU GLY SEQRES 11 A 301 GLY PRO ARG PRO THR HIS PHE ALA GLY VAL LEU THR VAL SEQRES 12 A 301 VAL LEU LYS LEU LEU GLN ILE VAL ARG PRO ASP ARG VAL SEQRES 13 A 301 PHE PHE GLY GLU LYS ASP TYR GLN GLN LEU VAL LEU ILE SEQRES 14 A 301 ARG GLN LEU VAL ALA ASP PHE ASN LEU ASP VAL ALA VAL SEQRES 15 A 301 VAL GLY VAL PRO THR VAL ARG GLU ALA ASP GLY LEU ALA SEQRES 16 A 301 MET SER SER ARG ASN ARG TYR LEU ASP PRO ALA GLN ARG SEQRES 17 A 301 ALA ALA ALA VAL ALA LEU SER ALA ALA LEU THR ALA ALA SEQRES 18 A 301 ALA HIS ALA ALA THR ALA GLY ALA GLN ALA ALA LEU ASP SEQRES 19 A 301 ALA ALA ARG ALA VAL LEU ASP ALA ALA PRO GLY VAL ALA SEQRES 20 A 301 VAL ASP TYR LEU GLU LEU ARG ASP ILE GLY LEU GLY PRO SEQRES 21 A 301 MET PRO LEU ASN GLY SER GLY ARG LEU LEU VAL ALA ALA SEQRES 22 A 301 ARG LEU GLY THR THR ARG LEU LEU ASP ASN ILE ALA ILE SEQRES 23 A 301 GLU ILE GLY THR PHE ALA GLY THR ASP ARG PRO ASP GLY SEQRES 24 A 301 TYR ARG SEQRES 1 B 301 ALA MET ALA ILE PRO ALA PHE HIS PRO GLY GLU LEU ASN SEQRES 2 B 301 VAL TYR SER ALA PRO GLY ASP VAL ALA ASP VAL SER ARG SEQRES 3 B 301 ALA LEU ARG LEU THR GLY ARG ARG VAL MET LEU VAL PRO SEQRES 4 B 301 THR MET GLY ALA LEU HIS GLU GLY HIS LEU ALA LEU VAL SEQRES 5 B 301 ARG ALA ALA LYS ARG VAL PRO GLY SER VAL VAL VAL VAL SEQRES 6 B 301 SER ILE PHE VAL ASN PRO MET GLN PHE GLY ALA GLY GLY SEQRES 7 B 301 ASP LEU ASP ALA TYR PRO ARG THR PRO ASP ASP ASP LEU SEQRES 8 B 301 ALA GLN LEU ARG ALA GLU GLY VAL GLU ILE ALA PHE THR SEQRES 9 B 301 PRO THR THR ALA ALA MET TYR PRO ASP GLY LEU ARG THR SEQRES 10 B 301 THR VAL GLN PRO GLY PRO LEU ALA ALA GLU LEU GLU GLY SEQRES 11 B 301 GLY PRO ARG PRO THR HIS PHE ALA GLY VAL LEU THR VAL SEQRES 12 B 301 VAL LEU LYS LEU LEU GLN ILE VAL ARG PRO ASP ARG VAL SEQRES 13 B 301 PHE PHE GLY GLU LYS ASP TYR GLN GLN LEU VAL LEU ILE SEQRES 14 B 301 ARG GLN LEU VAL ALA ASP PHE ASN LEU ASP VAL ALA VAL SEQRES 15 B 301 VAL GLY VAL PRO THR VAL ARG GLU ALA ASP GLY LEU ALA SEQRES 16 B 301 MET SER SER ARG ASN ARG TYR LEU ASP PRO ALA GLN ARG SEQRES 17 B 301 ALA ALA ALA VAL ALA LEU SER ALA ALA LEU THR ALA ALA SEQRES 18 B 301 ALA HIS ALA ALA THR ALA GLY ALA GLN ALA ALA LEU ASP SEQRES 19 B 301 ALA ALA ARG ALA VAL LEU ASP ALA ALA PRO GLY VAL ALA SEQRES 20 B 301 VAL ASP TYR LEU GLU LEU ARG ASP ILE GLY LEU GLY PRO SEQRES 21 B 301 MET PRO LEU ASN GLY SER GLY ARG LEU LEU VAL ALA ALA SEQRES 22 B 301 ARG LEU GLY THR THR ARG LEU LEU ASP ASN ILE ALA ILE SEQRES 23 B 301 GLU ILE GLY THR PHE ALA GLY THR ASP ARG PRO ASP GLY SEQRES 24 B 301 TYR ARG HET BZ2 A 301 12 HET GOL A 701 6 HET GOL A 702 6 HET EOH A 703 3 HET EOH A 704 3 HET BZ2 B 302 12 HETNAM BZ2 1-BENZOFURAN-2-CARBOXYLIC ACID HETNAM GOL GLYCEROL HETNAM EOH ETHANOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 BZ2 2(C9 H6 O3) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 EOH 2(C2 H6 O) FORMUL 9 HOH *248(H2 O) HELIX 1 1 ALA A 16 LEU A 29 1 14 HELIX 2 2 HIS A 44 ARG A 56 1 13 HELIX 3 3 THR A 85 GLY A 97 1 13 HELIX 4 4 THR A 105 TYR A 110 1 6 HELIX 5 5 GLY A 121 GLY A 130 5 10 HELIX 6 6 THR A 134 ARG A 151 1 18 HELIX 7 7 ASP A 161 PHE A 175 1 15 HELIX 8 8 SER A 196 LEU A 202 5 7 HELIX 9 9 ASP A 203 ALA A 210 1 8 HELIX 10 10 VAL A 211 ALA A 224 1 14 HELIX 11 11 GLY A 227 ALA A 241 1 15 HELIX 12 12 ALA B 16 THR B 30 1 15 HELIX 13 13 HIS B 44 VAL B 57 1 14 HELIX 14 14 THR B 85 GLY B 97 1 13 HELIX 15 15 THR B 105 TYR B 110 1 6 HELIX 16 16 GLY B 121 GLY B 130 5 10 HELIX 17 17 THR B 134 ARG B 151 1 18 HELIX 18 18 ASP B 161 PHE B 175 1 15 HELIX 19 19 SER B 196 LEU B 202 5 7 HELIX 20 20 ASP B 203 VAL B 211 1 9 HELIX 21 21 VAL B 211 ALA B 224 1 14 HELIX 22 22 GLY B 227 ALA B 241 1 15 SHEET 1 A 6 ASN A 12 TYR A 14 0 SHEET 2 A 6 ILE A 100 PHE A 102 1 O ALA A 101 N ASN A 12 SHEET 3 A 6 SER A 60 ILE A 66 1 N ILE A 66 O PHE A 102 SHEET 4 A 6 ARG A 33 THR A 39 1 N MET A 35 O VAL A 63 SHEET 5 A 6 ARG A 154 GLY A 158 1 O PHE A 156 N LEU A 36 SHEET 6 A 6 ALA A 180 VAL A 184 1 O VAL A 182 N VAL A 155 SHEET 1 B 2 THR A 117 GLN A 119 0 SHEET 2 B 2 THR B 117 GLN B 119 -1 O THR B 117 N GLN A 119 SHEET 1 C 3 ALA A 246 ASP A 254 0 SHEET 2 C 3 GLY A 264 LEU A 274 -1 O ARG A 267 N ARG A 253 SHEET 3 C 3 THR A 277 ILE A 287 -1 O ILE A 287 N GLY A 264 SHEET 1 D 6 ASN B 12 TYR B 14 0 SHEET 2 D 6 ILE B 100 PHE B 102 1 O ALA B 101 N ASN B 12 SHEET 3 D 6 SER B 60 ILE B 66 1 N ILE B 66 O PHE B 102 SHEET 4 D 6 ARG B 33 THR B 39 1 N MET B 35 O VAL B 63 SHEET 5 D 6 ARG B 154 GLY B 158 1 O ARG B 154 N LEU B 36 SHEET 6 D 6 ALA B 180 VAL B 184 1 O VAL B 182 N VAL B 155 SHEET 1 E 3 ALA B 246 ARG B 253 0 SHEET 2 E 3 GLY B 264 LEU B 274 -1 O LEU B 269 N GLU B 251 SHEET 3 E 3 THR B 277 ILE B 287 -1 O ILE B 283 N LEU B 268 CISPEP 1 ALA A 75 GLY A 76 0 0.62 CISPEP 2 GLY A 76 GLY A 77 0 -0.92 SITE 1 AC1 7 PRO A 38 THR A 39 MET A 40 HIS A 47 SITE 2 AC1 7 VAL A 143 GLN A 164 HOH A 518 SITE 1 AC2 9 MET A 109 TYR A 110 PRO A 111 ASP A 112 SITE 2 AC2 9 GLY A 113 ARG A 115 THR A 116 LYS A 145 SITE 3 AC2 9 ASP B 174 SITE 1 AC3 2 PRO A 111 ASP A 112 SITE 1 AC4 4 ARG A 115 THR A 117 GLN B 119 PRO B 120 SITE 1 AC5 3 THR A 218 HIS B 222 THR B 225 SITE 1 AC6 6 PRO B 38 THR B 39 MET B 40 HIS B 47 SITE 2 AC6 6 VAL B 143 GLN B 164 CRYST1 48.632 71.338 82.060 90.00 99.51 90.00 P 1 21 1 4 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 0.020563 0.000000 0.003445 0.00000 SCALE2 0.000000 0.014018 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012356 0.00000