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- PDB-4uho: Characterization of a Novel Transaminase from Pseudomonas sp. Str... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4uho | ||||||
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Title | Characterization of a Novel Transaminase from Pseudomonas sp. Strain AAC | ||||||
![]() | OMEGA AMINO ACID-PYRUVATE AMINOTRANSFERASE | ||||||
![]() | TRANSFERASE / BIOCATALYSIS / AMINOTRANSFERASE / PYRIDOXAL-5'-PHOSPHATE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wilding, M. / Peat, T.S. / Newman, J. / Scott, C. | ||||||
![]() | ![]() Title: A Beta-Alanine Catabolism Pathway Containing a Highly Promiscuous Omega-Transaminase in the 12-Aminododecanate-Degrading Pseudomonas Sp. Strain Aac. Authors: Wilding, M. / Peat, T.S. / Newman, J. / Scott, 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 | ![]() | 223.1 KB | Display | ![]() |
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PDB format | ![]() | 178.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 490.9 KB | Display | ![]() |
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Full document | ![]() | 496.1 KB | Display | |
Data in XML | ![]() | 25.5 KB | Display | |
Data in CIF | ![]() | 39.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4uhmSC ![]() 4uhnC 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 50360.105 Da / Num. of mol.: 1 / Fragment: FULL ENZYME Source method: isolated from a genetically manipulated source Details: SEQUENCE HAS AN N-TERMINAL HIS-TAG AND THROMBIN SITE ADDED. Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A081YAY5, beta-alanine-pyruvate transaminase |
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-Non-polymers , 8 types, 635 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-UNL / Num. of mol.: 1 / Source method: obtained synthetically | ||||||||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PLP / | #7: Chemical | ChemComp-PEG / | #8: Chemical | ChemComp-EOH / | #9: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | UNKNOWN LIGAND (UNL): UNKNOWN DENSITY- JUST GUESSED AT ATOMS |
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Sequence details | SEQUENCE HAS AN N-TERMINAL HIS-TAG AND THROMBIN SITE ADDED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.9 % / Description: NONE |
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Crystal grow | pH: 7 Details: PROTEIN WAS AT 8 MG/ML, DROPS WERE 200 NL PLUS 200 NL WITH THE RESERVOIR SOLUTION MADE UP OF 10% PEG 4000, 0.2 M MGCL2, 0.1 M TRIS PH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→44.9 Å / Num. obs: 144518 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.24→1.26 Å / Redundancy: 7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.8 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4UHM Resolution: 1.24→89.77 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.989 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY STRONG UNKNOWN DENSITY IN STRUCTURE WAS MODELLED AS AN UNKNOWN LIGAND.
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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: 11.226 Å2
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Refinement step | Cycle: LAST / Resolution: 1.24→89.77 Å
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Refine LS restraints |
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