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Yorodumi- PDB-3t8a: Crystal structure of Mycobacterium tuberculosis MenB in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t8a | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis MenB in complex with substrate analogue, OSB-NCoA | ||||||
Components | 1,4-Dihydroxy-2-naphthoyl-CoA synthase | ||||||
Keywords | LYASE/LYASE INHIBITOR / crotonase superfamily / LYASE-LYASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 1,4-dihydroxy-2-naphthoyl-CoA synthase / 1,4-dihydroxy-2-naphthoyl-CoA synthase activity / menaquinone biosynthetic process / protein hexamerization / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.245 Å | ||||||
Authors | Li, H.-J. / Li, X. / Liu, N. / Zhang, H. / Truglio, J. / Mishra, S. / Kisker, C. / Garcia-Diaz, M. / Tonge, P. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Mechanism of the Intramolecular Claisen Condensation Reaction Catalyzed by MenB, a Crotonase Superfamily Member. Authors: Li, H.J. / Li, X. / Liu, N. / Zhang, H. / Truglio, J.J. / Mishra, S. / Kisker, C. / Garcia-Diaz, M. / Tonge, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t8a.cif.gz | 166.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t8a.ent.gz | 128.3 KB | Display | PDB format |
PDBx/mmJSON format | 3t8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t8a_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3t8a_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3t8a_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 3t8a_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/3t8a ftp://data.pdbj.org/pub/pdb/validation_reports/t8/3t8a | HTTPS FTP |
-Related structure data
Related structure data | 3t88C 3t89C 3t8bC 1q51S C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 36903.301 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0548c / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): CodonPlus References: UniProt: O06414, UniProt: P9WNP5*PLUS, 1,4-dihydroxy-2-naphthoyl-CoA synthase #2: Chemical | #3: 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: 2.05 Å3/Da / Density % sol: 40.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 19% PEG6000, 300 mM sodium chloride, 100 mM HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock double crystal sagittal focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.245→50 Å / Num. obs: 45905 / % possible obs: 99.6 % / Redundancy: 15.2 % / Rmerge(I) obs: 0.113 / Χ2: 1.071 / Net I/σ(I): 7.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q51 Resolution: 2.245→46.607 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 2.4 / σ(F): 0.23 / Phase error: 21.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.854 Å2 / ksol: 0.396 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.08 Å2 / Biso mean: 37.9204 Å2 / Biso min: 17.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.245→46.607 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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