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Yorodumi- PDB-3le8: Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3le8 | ||||||
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Title | Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.70 Angstrom resolution in complex with 2-(2-((benzofuran-2-carboxamido)methyl)-5-methoxy-1H-indol-1-yl)acetic acid | ||||||
Components | Pantothenate synthetase | ||||||
Keywords | LIGASE / Fragment-based drug discovery / ILOE / fragment linking / ATP-binding / Cytoplasm / Magnesium / Metal-binding / Nucleotide-binding / Pantothenate biosynthesis | ||||||
Function / homology | Function and homology information beta-alanine metabolic process / pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / manganese ion binding / magnesium ion binding / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Silvestre, H.L. / Hung, A.W. / Sledz, P. / Ciulli, A. / Blundell, T.L. / Abell, C. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Optimization of the interligand overhauser effect for fragment linking: application to inhibitor discovery against Mycobacterium tuberculosis pantothenate synthetase. Authors: Sledz, P. / Silvestre, H.L. / Hung, A.W. / Ciulli, A. / Blundell, T.L. / Abell, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3le8.cif.gz | 136.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3le8.ent.gz | 106.3 KB | Display | PDB format |
PDBx/mmJSON format | 3le8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3le8_validation.pdf.gz | 1016.9 KB | Display | wwPDB validaton report |
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Full document | 3le8_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3le8_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 3le8_validation.cif.gz | 47.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/3le8 ftp://data.pdbj.org/pub/pdb/validation_reports/le/3le8 | HTTPS FTP |
-Related structure data
Related structure data | 3iubS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31500.100 Da / Num. of mol.: 2 / Mutation: T2A, E77G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT3707, MTCY07H7B.20, panC, Rv3602c / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (rosetta 2) References: UniProt: P0A5R0, UniProt: P9WIL5*PLUS, pantoate-beta-alanine ligase (AMP-forming) |
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-Non-polymers , 5 types, 595 molecules
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EOH / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 12-14% PEG 3000, 100-150 mM Li2SO4, 100-150 mM Imidazole, 2-4% Ethanol, 5-10% Glycerol, 20 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2009 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→38.63 Å / Num. obs: 59906 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8768 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IUB Resolution: 1.7→38.63 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.562 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.578 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→38.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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