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Yorodumi- PDB-5dic: Fatty acid binding protein OBP56a from the oral disk of the blowf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dic | ||||||
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Title | Fatty acid binding protein OBP56a from the oral disk of the blowfly Phormia regina | ||||||
Components | Odorant-binding protein | ||||||
Keywords | Odorant-binding protein / Palmitate olfaction odorant | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Phormia regina (black blowfly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.185 Å | ||||||
Authors | Ishida, Y. / Leal, W.S. / Wilson, D.K. | ||||||
Citation | Journal: To Be Published Title: In preparation Authors: Ishida, Y. / Leal, W.S. / Wilson, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dic.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dic.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 5dic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dic_validation.pdf.gz | 737.5 KB | Display | wwPDB validaton report |
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Full document | 5dic_full_validation.pdf.gz | 737.6 KB | Display | |
Data in XML | 5dic_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 5dic_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/5dic ftp://data.pdbj.org/pub/pdb/validation_reports/di/5dic | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13276.255 Da / Num. of mol.: 1 / Fragment: UNP residues 19-135 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phormia regina (black blowfly) / Gene: PregOBP56a / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: L8B8J6 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 20% PEG 6000, 1M LiCl, 100mM citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→28.1 Å / Num. obs: 34518 / % possible obs: 87.4 % / Redundancy: 2.48 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.18→1.22 Å / Rmerge(I) obs: 0.176 |
-Processing
Software |
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Refinement | Resolution: 1.185→28.1 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.003 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.039 / 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: 19.525 Å2
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Refinement step | Cycle: 1 / Resolution: 1.185→28.1 Å
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Refine LS restraints |
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