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Yorodumi- PDB-6gio: Structure of Amino Acid Amide Racemase from Ochrobactrum anthropi -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gio | ||||||
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Title | Structure of Amino Acid Amide Racemase from Ochrobactrum anthropi | ||||||
Components | Amino acid amide racemase | ||||||
Keywords | ISOMERASE / PLP / amino acid / amino acid amide / amino acid ester / racemase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ochrobactrum anthropi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Frese, A. / Grogan, G. | ||||||
Citation | Journal: Chembiochem / Year: 2018 Title: An Aminocaprolactam Racemase from Ochrobactrum anthropi with Promiscuous Amino Acid Ester Racemase Activity. Authors: Frese, A. / Barrass, S.V. / Sutton, P.W. / Adams, 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 | 6gio.cif.gz | 334.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gio.ent.gz | 271 KB | Display | PDB format |
PDBx/mmJSON format | 6gio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/6gio ftp://data.pdbj.org/pub/pdb/validation_reports/gi/6gio | HTTPS FTP |
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-Related structure data
Related structure data | 5m46S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 46862.535 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ochrobactrum anthropi (bacteria) / Gene: aaarA / Production host: Escherichia coli (E. coli) / References: UniProt: Q06K28 #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-EDO / | #4: 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: 2.07 Å3/Da / Density % sol: 40.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M HEPES, pH 7.0 2ith 0.2 M MgCl2 and 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→64.6 Å / Num. obs: 123230 / % possible obs: 98.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 28 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.09 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.87→1.92 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 9034 / CC1/2: 0.55 / Rpim(I) all: 0.77 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M46 Resolution: 1.87→64.6 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.491 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.15 / 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: 29.057 Å2
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Refinement step | Cycle: 1 / Resolution: 1.87→64.6 Å
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Refine LS restraints |
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