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Yorodumi- PDB-3lv2: Crystal structure of Mycobacterium tuberculosis 7,8-diaminopelarg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lv2 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis 7,8-diaminopelargonic acid synthase in complex with substrate analog sinefungin | ||||||
Components | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | ||||||
Keywords | TRANSFERASE / Rv1568 / aminotransferase / bioA / 7 / 8-diaminopelargonic acid synthase / Biotin biosynthesis / Pyridoxal phosphate / S-adenosyl-L-methionine | ||||||
Function / homology | Function and homology information adenosylmethionine-8-amino-7-oxononanoate transaminase / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||
Authors | Dey, S. / Sacchettini, J.C. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase . Authors: Dey, S. / Lane, J.M. / Lee, R.E. / Rubin, E.J. / Sacchettini, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lv2.cif.gz | 177.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lv2.ent.gz | 137.8 KB | Display | PDB format |
PDBx/mmJSON format | 3lv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/3lv2 ftp://data.pdbj.org/pub/pdb/validation_reports/lv/3lv2 | HTTPS FTP |
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-Related structure data
Related structure data | 3bv0SC 3dodC 3drdC 3du4C 3fgnC 3fmfC 3fmiC 3fpaC 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: 49226.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: bioA, MT1619, MTCY336.35c, Rv1568 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) References: UniProt: P0A4X6, UniProt: P9WQ81*PLUS, adenosylmethionine-8-amino-7-oxononanoate transaminase #2: Chemical | #3: Chemical | ChemComp-SFG / | #4: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT H315R WAS A NATURAL MUTATION | |
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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: 2.1 Å3/Da / Density % sol: 41.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 20% PEGMME 5000, 0.1M bistris buffer, pH 7.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→50 Å / Num. obs: 43477 / % possible obs: 98.7 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 33.4 |
Reflection shell | Resolution: 2.18→2.3 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 7 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BV0 Resolution: 2.18→35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.935 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 27.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.18→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.235 Å / Total num. of bins used: 20
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