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Yorodumi- PDB-5g0a: The crystal structure of a S-selective transaminase from Bacillus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g0a | ||||||
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Title | The crystal structure of a S-selective transaminase from Bacillus megaterium | ||||||
Components | TRANSAMINASE | ||||||
Keywords | TRANSFERASE / TRANSAMINASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BACILLUS MEGATERIUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 | 5g0a.cif.gz | 395.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g0a.ent.gz | 325.3 KB | Display | PDB format |
PDBx/mmJSON format | 5g0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/5g0a ftp://data.pdbj.org/pub/pdb/validation_reports/g0/5g0a | HTTPS FTP |
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-Related structure data
Related structure data | 5g09C 5g2pC 5g2qC 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 54264.293 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: PYRIDOXAL-5'-PHOSPHATE COVALENTLY BOUND TO LYSINE 298 Source: (gene. exp.) BACILLUS MEGATERIUM (bacteria) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA II References: UniProt: A0A0Q9UXH6, Transferases; Transferring nitrogenous groups; Transaminases |
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-Non-polymers , 6 types, 1116 molecules
#2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-1PE / #4: Chemical | ChemComp-PEG / #5: Chemical | #6: Chemical | ChemComp-PG4 / #7: Water | ChemComp-HOH / | |
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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: 2.17 Å3/Da / Density % sol: 43.5 % / Description: NONE |
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Crystal grow | pH: 4.2 Details: 30% PEG300 50 MM NA-PHOSPHATE/CITRATE, PH 4.2 10 MM PYRIDOXAL-5-PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: MARRESEARCH MAR-225MM / Detector: CCD / Date: Feb 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→43.4 Å / Num. obs: 200029 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.6 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GJU Resolution: 1.7→43.42 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.227 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.523 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→43.42 Å
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Refine LS restraints |
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