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Yorodumi- PDB-5m46: Alpha-amino epsilon-caprolactam racemase (ACLR) from Rhizobacteri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m46 | ||||||
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Title | Alpha-amino epsilon-caprolactam racemase (ACLR) from Rhizobacterium freirei | ||||||
Components | Aminotransferase class-III | ||||||
Keywords | ISOMERASE / PLP / racemase | ||||||
Function / homology | Function and homology information L-alanine catabolic process, by transamination / alanine-glyoxylate transaminase activity / glyoxylate catabolic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Rhizobium freirei PRF 81 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Frese, A. / Sutton, P.W. / Turkenburg, J.P. / Grogan, G. | ||||||
Citation | Journal: Acs Catalysis / Year: 2017 Title: Snapshots of the Catalytic Cycle of the Industrial Enzyme alpha-Amino-epsilon-Caprolactam Racemase (ACLR) Observed Using X-ray Crystallography Authors: Frese, A. / Sutton, P.W. / Turkenburg, J.P. / Grogan, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m46.cif.gz | 98.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m46.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 5m46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m46_validation.pdf.gz | 455.9 KB | Display | wwPDB validaton report |
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Full document | 5m46_full_validation.pdf.gz | 458.8 KB | Display | |
Data in XML | 5m46_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 5m46_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/5m46 ftp://data.pdbj.org/pub/pdb/validation_reports/m4/5m46 | HTTPS FTP |
-Related structure data
Related structure data | 5m49C 5m4bC 5m4dC 2zukS 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
#1: Protein | Mass: 46046.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium freirei PRF 81 (bacteria) / Gene: RHSP_08934 / Plasmid: pET-YSBLIC-3C / Production host: Escherichia coli BL21(DE3) / References: UniProt: N6UXY4 | ||
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#2: Chemical | ChemComp-PLP / | ||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.27 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M MgCl2, 25 % PEG 3350, 0.1 mM HEPES (pH 7.0). |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→45.24 Å / Num. obs: 44637 / % possible obs: 98.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.62→1.65 Å / Rmerge(I) obs: 0.628 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZUK Resolution: 1.62→45.24 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.766 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.084 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→45.24 Å
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Refine LS restraints |
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