+Open data
-Basic information
Entry | Database: PDB / ID: 4ysn | ||||||
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Title | Structure of aminoacid racemase in complex with PLP | ||||||
Components | Putative 4-aminobutyrate aminotransferase | ||||||
Keywords | ISOMERASE / fold type I of PLP-dependent enzyme | ||||||
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: 1.94 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 | 4ysn.cif.gz | 376.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ysn.ent.gz | 302.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ysn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ysn_validation.pdf.gz | 476.4 KB | Display | wwPDB validaton report |
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Full document | 4ysn_full_validation.pdf.gz | 492.8 KB | Display | |
Data in XML | 4ysn_validation.xml.gz | 75.6 KB | Display | |
Data in CIF | 4ysn_validation.cif.gz | 111.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/4ysn ftp://data.pdbj.org/pub/pdb/validation_reports/ys/4ysn | HTTPS FTP |
-Related structure data
Related structure data | 4ysvC 5wyaC 5wyfC 2eo5S 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
#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 #2: Chemical | ChemComp-PLP / #3: 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: 2.25 Å3/Da / Density % sol: 45.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2-propanol, Mg acetate, cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 29, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.94→50 Å / Num. obs: 132236 / % possible obs: 99.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.111 / Χ2: 4.58 / Net I/av σ(I): 41.452 / Net I/σ(I): 15.6 / Num. measured all: 885535 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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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: 2EO5 Resolution: 1.94→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.865 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93 Å2 / Biso mean: 21.97 Å2 / Biso min: 10.11 Å2
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Refinement step | Cycle: final / Resolution: 1.94→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.99 Å / Total num. of bins used: 20
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