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- PDB-3lv2: Crystal structure of Mycobacterium tuberculosis 7,8-diaminopelarg... -
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Open data
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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 | ||||||
![]() | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | ||||||
![]() | TRANSFERASE / Rv1568 / aminotransferase / bioA / 7 / 8-diaminopelargonic acid synthase / Biotin biosynthesis / Pyridoxal phosphate / S-adenosyl-L-methionine | ||||||
Function / homology | ![]() adenosylmethionine-8-amino-7-oxononanoate transaminase / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / dethiobiotin synthase activity / biotin biosynthetic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dey, S. / Sacchettini, J.C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.6 KB | Display | ![]() |
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PDB format | ![]() | 137.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 699 KB | Display | ![]() |
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Full document | ![]() | 714.9 KB | Display | |
Data in XML | ![]() | 35.1 KB | Display | |
Data in CIF | ![]() | 49.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bv0SC ![]() 3dodC ![]() 3drdC ![]() 3du4C ![]() 3fgnC ![]() 3fmfC ![]() 3fmiC ![]() 3fpaC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() 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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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