+Open data
-Basic information
Entry | Database: PDB / ID: 5wyf | ||||||
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Title | Structure of amino acid racemase, 2.12 A | ||||||
Components | Isoleucine 2-epimerase | ||||||
Keywords | ISOMERASE / PLP-dependent enzyme / fold type I | ||||||
Function / homology | Function and homology information isoleucine 2-epimerase / transaminase activity / isomerase activity / pyridoxal phosphate binding / identical protein binding Similarity search - Function | ||||||
Biological species | Lactobacillus buchneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.12 Å | ||||||
Authors | Sakuraba, H. / Mutaguchi, Y. / Hayashi, J. / Ohshima, T. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 Title: Crystal structure of the novel amino-acid racemase isoleucine 2-epimerase from Lactobacillus buchneri. Authors: Hayashi, J. / Mutaguchi, Y. / Minemura, Y. / Nakagawa, N. / Yoneda, K. / Ohmori, T. / Ohshima, T. / Sakuraba, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wyf.cif.gz | 360.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wyf.ent.gz | 290.7 KB | Display | PDB format |
PDBx/mmJSON format | 5wyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wyf_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 5wyf_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 5wyf_validation.xml.gz | 66.4 KB | Display | |
Data in CIF | 5wyf_validation.cif.gz | 92.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/5wyf ftp://data.pdbj.org/pub/pdb/validation_reports/wy/5wyf | HTTPS FTP |
-Related structure data
Related structure data | 4ysnC 4ysvC 5wyaSC 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
#1: Protein | Mass: 50708.566 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus buchneri (bacteria) / Plasmid: pCold ProS2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: M1GRN3, isoleucine 2-epimerase #2: Chemical | ChemComp-ILP / #3: Chemical | ChemComp-CD / #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: 2.37 Å3/Da / Density % sol: 48.2 % / Mosaicity: 0.347 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Cadmium sulfate hydrate, Sodium acetate, Hepes |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.12→50 Å / Num. obs: 104213 / % possible obs: 99.3 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.034 / Rrim(I) all: 0.088 / Χ2: 0.665 / Net I/σ(I): 5.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WYA Resolution: 2.12→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.188 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.182 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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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 max: 116.52 Å2 / Biso mean: 37.575 Å2 / Biso min: 19.71 Å2
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Refinement step | Cycle: final / Resolution: 2.12→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.121→2.176 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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