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- PDB-4a6r: Crystal structure of the omega transaminase from Chromobacterium ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4a6r | ||||||
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Title | Crystal structure of the omega transaminase from Chromobacterium violaceum in the apo form, crystallised from polyacrylic acid | ||||||
![]() | OMEGA TRANSAMINASE | ||||||
![]() | TRANSFERASE / PLP-BINDING ENZYME / TRANSAMINASE FOLD TYPE I | ||||||
Function / homology | ![]() adenosylmethionine-8-amino-7-oxononanoate transaminase activity / pyridoxal phosphate binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Logan, D.T. / Hakansson, M. / Yengo, K. / Svedendahl Humble, M. / Engelmark Cassimjee, K. / Walse, B. / Abedi, V. / Federsel, H.-J. / Berglund, P. | ||||||
![]() | ![]() Title: Crystal Structures of the Chromobacterium Violaceum Omega-Transaminase Reveal Major Structural Rearrangements Upon Binding of Coenzyme Plp. Authors: Svedendahl Humble, M. / Engelmark Cassimjee, K. / Hakansson, M. / Kimbung, Y.R. / Walse, B. / Abedi, V. / Federsel, H.-J. / Berglund, P. / Logan, D.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 352.9 KB | Display | ![]() |
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PDB format | ![]() | 288.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 40.4 KB | Display | |
Data in CIF | ![]() | 61.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4a6tC ![]() 4a6uC ![]() 4a72C ![]() 3hmuS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9972, -0.05709, 0.04849), 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, adenosylmethionine-8-amino-7-oxononanoate transaminase #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | POLYACRYLI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.9 % / Description: NONE |
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Crystal grow | pH: 7.4 Details: 0.2 M MGCL2, 0.1 M HEPES PH 7.5, 22% W/V POLYACRYLIC ACID 5100 SODIUM SALT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD / Date: Apr 16, 2011 / Details: MULTILAYER MIRROR, VERTICALLY FOCUSING |
Radiation | Monochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0397 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. obs: 690977 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 10.87 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.35→1.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.9 / % possible all: 89.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3HMU Resolution: 1.349→23.287 Å / SU ML: 0.15 / σ(F): 1.99 / Phase error: 15.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.043 Å2 / ksol: 0.39 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.349→23.287 Å
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Refine LS restraints |
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LS refinement shell |
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