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Yorodumi- PDB-4uhn: Characterization of a Novel Transaminase from Pseudomonas sp. Str... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uhn | ||||||
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Title | Characterization of a Novel Transaminase from Pseudomonas sp. Strain AAC | ||||||
Components | OMEGA AMINO ACID-PYRUVATE AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE / BIOCATALYSIS / AMINOTRANSFERASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PSEUDOMONAS SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Wilding, M. / Peat, T.S. / Newman, J. / Scott, C. | ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uhn.cif.gz | 187.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uhn.ent.gz | 149.1 KB | Display | PDB format |
PDBx/mmJSON format | 4uhn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/4uhn ftp://data.pdbj.org/pub/pdb/validation_reports/uh/4uhn | HTTPS FTP |
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-Related structure data
Related structure data | 4uhmSC 4uhoC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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: 50520.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SEQUENCE HAS AN N-TERMINAL HIS-TAG AND THROMBIN SITE ADDED. IN ADDITION, IT WAS FOUND THAT TWO OF THE HISTIDINE RESIDUES WERE PHOSPHORYLATED. Source: (gene. exp.) PSEUDOMONAS SP. (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: A0A081YAY5, beta-alanine-pyruvate transaminase |
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-Non-polymers , 6 types, 195 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-ACY / |
#5: Chemical | ChemComp-PLP / |
#6: Chemical | ChemComp-NA / |
#7: Water | ChemComp-HOH / |
-Details
Sequence details | SEQUENCE HAS AN N-TERMINAL HIS-TAG AND THROMBIN SITE ADDED. IN ADDITION, THERE ARE TWO ...SEQUENCE HAS AN N-TERMINAL HIS-TAG AND THROMBIN SITE ADDED. IN ADDITION, THERE ARE TWO PHOSPHORYL |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.8 % / Description: NONE |
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Crystal grow | pH: 8 Details: PROTEIN WAS AT 10 MG/ML AND WAS SET UP IN 200 NL PLUS 200 NL DROPS AGAINST 2.5 M NACL, 20 MM ZINC ACETATE, 0.1 M IMIDAZOLE BUFFER AT PH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9191 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9191 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→44.7 Å / Num. obs: 25807 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Rmerge(I) obs: 0.27 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.21→2.28 Å / Redundancy: 14.8 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4UHM Resolution: 2.21→89.34 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.59 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED THE PHOSPHO-HISTIDINE RESIDUES WERE FOUND IN THE ELECTRON DENSITY MAPS AT POSITIONS 31 AND 360 IN THE SEQUENCE AND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED THE PHOSPHO-HISTIDINE RESIDUES WERE FOUND IN THE ELECTRON DENSITY MAPS AT POSITIONS 31 AND 360 IN THE SEQUENCE AND LATER VERIFIED VIA ASSAY.
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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: 23.106 Å2
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Refinement step | Cycle: LAST / Resolution: 2.21→89.34 Å
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Refine LS restraints |
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