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Yorodumi- PDB-5g2q: The crystal structure of a S-selective transaminase from Arthroba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g2q | ||||||
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Title | The crystal structure of a S-selective transaminase from Arthrobacter sp. with alanine bound | ||||||
Components | TRANSAMINASE | ||||||
Keywords | TRANSFERASE / TRANSAMINASE | ||||||
Function / homology | Function and homology information Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ARTHROBACTER SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | van Oosterwijk, N. / Willies, S. / Hekelaar, J. / Terwisscha van Scheltinga, A.C. / Turner, N.J. / Dijkstra, B.W. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Structural Basis of Substrate Range and Enantioselectivity of Two S-Selective Omega- Transaminases Authors: Van Oosterwijk, N. / Willies, S. / Hekelaar, J. / Terwisscha Van Scheltinga, A.C. / Turner, N.J. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g2q.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5g2q.ent.gz | 1.8 MB | Display | PDB format |
PDBx/mmJSON format | 5g2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/5g2q ftp://data.pdbj.org/pub/pdb/validation_reports/g2/5g2q | HTTPS FTP |
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-Related structure data
Related structure data | 5g09C 5g0aC 5g2pC 3gjuS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 54203.145 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: PYRIDOXAL-5'-PHOSPHATE COVALENTLY BOUND ALANINE / Source: (gene. exp.) ARTHROBACTER SP. (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 References: UniProt: A0A1C7D191*PLUS, Transferases; Transferring nitrogenous groups; Transaminases #2: Chemical | ChemComp-PDA / #3: Water | ChemComp-HOH / | Nonpolymer details | ALANINE COVALENTLY | |
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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: 2.09 Å3/Da / Density % sol: 41.25 % / Description: NONE |
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Crystal grow | pH: 5 Details: 15% PEG 3350 0.2 M NA-MALONATE 100 MM MMT BUFFER (DL-MALIC ACID, MES AND TRIS BASE) PH 5.0, 10 MM PLP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.71 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.71 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→43 Å / Num. obs: 214456 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.8 / % possible all: 87.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GJU Resolution: 2.3→47.96 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Refinement step | Cycle: LAST / Resolution: 2.3→47.96 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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