+Open data
-Basic information
Entry | Database: PDB / ID: 3wmr | ||||||
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Title | Crystal structure of VinJ | ||||||
Components | Proline iminopeptidase | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces halstedii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Shinohara, Y. / Miyanaga, A. / Kudo, F. / Eguchi, T. | ||||||
Citation | Journal: Febs Lett. / Year: 2014 Title: The crystal structure of the amidohydrolase VinJ shows a unique hydrophobic tunnel for its interaction with polyketide substrates Authors: Shinohara, Y. / Miyanaga, A. / Kudo, F. / Eguchi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wmr.cif.gz | 359.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wmr.ent.gz | 293.6 KB | Display | PDB format |
PDBx/mmJSON format | 3wmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wmr_validation.pdf.gz | 460.9 KB | Display | wwPDB validaton report |
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Full document | 3wmr_full_validation.pdf.gz | 464.5 KB | Display | |
Data in XML | 3wmr_validation.xml.gz | 37 KB | Display | |
Data in CIF | 3wmr_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/3wmr ftp://data.pdbj.org/pub/pdb/validation_reports/wm/3wmr | HTTPS FTP |
-Related structure data
Related structure data | 3nwoS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 35703.352 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces halstedii (bacteria) / Gene: vinJ / Production host: Escherichia coli (E. coli) / References: UniProt: Q76KY6 #2: Chemical | #3: Chemical | #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: 2.38 Å3/Da / Density % sol: 48.29 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M lithium acetate, 20% polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-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 7, 2012 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50.96 Å / Num. all: 71740 / Num. obs: 63636 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.95→2 Å / % possible all: 65.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NWO Resolution: 1.95→50.96 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.533 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.151 / 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 mean: 30.224 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→50.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.952→2.003 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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