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- PDB-4ba4: Crystal structure of the apo omega-transaminase from Chromobacter... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ba4 | ||||||
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Title | Crystal structure of the apo omega-transaminase from Chromobacterium violaceum | ||||||
![]() | AMINOTRANSFERASE | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() adenosylmethionine-8-amino-7-oxononanoate transaminase activity / pyridoxal phosphate binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sayer, C. / Isupov, M.N. / Littlechild, J.A. | ||||||
![]() | ![]() Title: Structural Studies with Pseudomonas and Chromobacterium [Omega]-Aminotransferases Provide Insights Into Their Differing Substrate Specificity. Authors: Sayer, C. / Isupov, M.N. / Westlake, A. / Littlechild, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201.9 KB | Display | ![]() |
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PDB format | ![]() | 161.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.6 KB | Display | ![]() |
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Full document | ![]() | 452.3 KB | Display | |
Data in XML | ![]() | 40.5 KB | Display | |
Data in CIF | ![]() | 62.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ah3C ![]() 4b98C ![]() 4b9bC ![]() 4ba5C ![]() 1qj3S 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.998, 0.062, 0.023), Vector: |
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Components
#1: Protein | Mass: 51279.293 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q7NWG4, beta-alanine-pyruvate transaminase #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.4 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→14 Å / Num. obs: 74538 / % possible obs: 90.7 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 1.73→1.82 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.4 / % possible all: 81.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QJ3 Resolution: 1.73→60.75 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.391 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.129 / 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: 31.868 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→60.75 Å
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Refine LS restraints |
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