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- PDB-3drd: Crystal Structure of 7,8 Diaminopelargonic Acid Synthase Apoenzym... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3drd | ||||||
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Title | Crystal Structure of 7,8 Diaminopelargonic Acid Synthase Apoenzyme in Bacillus subtilis | ||||||
![]() | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | ||||||
![]() | TRANSFERASE / aminotransferase / biotin biosynthesis / pyridoxal phosphate / s-adenosyl-l-methionine | ||||||
Function / homology | ![]() lysine-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 | ![]() | 175.7 KB | Display | ![]() |
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PDB format | ![]() | 139.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441 KB | Display | ![]() |
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Full document | ![]() | 461 KB | Display | |
Data in XML | ![]() | 33.9 KB | Display | |
Data in CIF | ![]() | 47.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bv0SC ![]() 3dodC ![]() 3du4C ![]() 3fgnC ![]() 3fmfC ![]() 3fmiC ![]() 3fpaC ![]() 3lv2C C: citing same article ( S: Starting model for refinement |
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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: 50174.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P53555, adenosylmethionine-8-amino-7-oxononanoate transaminase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.66 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG3350, 0.2M SODIUM THIOCYANATE, 5% XYLITOL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 28, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→39.53 Å / Num. obs: 41693 / % possible obs: 93 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 2.17→2.29 Å / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3.8 / % possible all: 63.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3BV0 Resolution: 2.17→35 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.889 / SU B: 6.312 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.249 / 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: 27.434 Å2
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Refinement step | Cycle: LAST / Resolution: 2.17→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.17→2.226 Å / Total num. of bins used: 20
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