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Yorodumi- PDB-4pt1: Crystal structure of Locusta migratoria odorant binding proteins ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pt1 | ||||||
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Title | Crystal structure of Locusta migratoria odorant binding proteins lmigOBP1 | ||||||
Components | Odorant-binding protein 1d | ||||||
Keywords | TRANSPORT PROTEIN / OBP / odorant perception | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Locusta migratoria (migratory locust) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Zheng, J. / Li, J. / Chen, Z. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2015 Title: Crystal structure of the Locusta migratoria odorant binding protein. Authors: Zheng, J. / Li, J. / Han, L. / Wang, Y. / Wu, W. / Qi, X. / Tao, Y. / Zhang, L. / Zhang, Z. / Chen, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pt1.cif.gz | 113 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pt1.ent.gz | 93.9 KB | Display | PDB format |
PDBx/mmJSON format | 4pt1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pt1_validation.pdf.gz | 445.6 KB | Display | wwPDB validaton report |
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Full document | 4pt1_full_validation.pdf.gz | 448.2 KB | Display | |
Data in XML | 4pt1_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 4pt1_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/4pt1 ftp://data.pdbj.org/pub/pdb/validation_reports/pt/4pt1 | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14988.765 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Locusta migratoria (migratory locust) / Gene: lmigobp1 / Plasmid: pet-22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q3HM32 #2: Chemical | ChemComp-PG0 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6 Details: 25% PEG 3350, pH 6, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 130 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: Dec 6, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 26355 / Num. obs: 23722 / % possible obs: 90 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 1.65→1.68 Å / % possible all: 51 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.383 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.279 / ESU R Free: 0.124 / 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: 16.379 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.653→1.696 Å / Total num. of bins used: 20
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