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Yorodumi- PDB-4bfu: Crystal structure of Mycobacterium tuberculosis PanK in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bfu | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis PanK in complex with a triazole inhibitory compound (1c) and phosphate | ||||||
Components | PANTOTHENATE KINASE | ||||||
Keywords | TRANSFERASE / COA PATHWAY / INHIBITOR | ||||||
Function / homology | Function and homology information pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Bjorkelid, C. / Bergfors, T. / Jones, T.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural and Biochemical Characterization of Compounds Inhibiting Mycobacterium Tuberculosis Pank Authors: Bjorkelid, C. / Bergfors, T. / Raichurkar, A.K.V. / Mukherjee, K. / Krishnan, M. / Bandodkar, B. / Jones, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bfu.cif.gz | 138.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bfu.ent.gz | 109.2 KB | Display | PDB format |
PDBx/mmJSON format | 4bfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bfu_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4bfu_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4bfu_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 4bfu_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/4bfu ftp://data.pdbj.org/pub/pdb/validation_reports/bf/4bfu | HTTPS FTP |
-Related structure data
Related structure data | 4bfsSC 4bftC 4bfvC 4bfwC 4bfxC 4bfyC 4bfzC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36533.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P63810, UniProt: P9WPA7*PLUS, pantothenate kinase #2: Chemical | #3: Chemical | #4: 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: 2.96 Å3/Da / Density % sol: 58.43 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: SITTING-DROP VAPOR-DIFFUSION METHOD AT 293 K. 1.8 M SODIUM/POTASSIUM PHOSPHATE, PH 8.2 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 7, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→60 Å / Num. obs: 39320 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.28→2.4 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.7 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BFS Resolution: 2.28→57.46 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.957 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.227 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.214 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→57.46 Å
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Refine LS restraints |
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