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Yorodumi- PDB-2wch: Structure of BMori GOBP2 (General Odorant Binding Protein 2) with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wch | ||||||
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Title | Structure of BMori GOBP2 (General Odorant Binding Protein 2) with bombykal | ||||||
Components | GENERAL ODORANT-BINDING PROTEIN 1 | ||||||
Keywords | TRANSPORT PROTEIN / ODORANT BINDING PROTEIN / OLFACTION / TRANSPORT / DISULFIDE BOND / INSECT PHEREMONE / SENSORY TRANSDUCTION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BOMBYX MORI (domestic silkworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Robertson, G. / Zhou, J.-J. / He, X. / Pickett, J.A. / Field, L.M. / Keep, N.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Characterisation of Bombyx Mori Odorant-Binding Proteins Reveals that a General Odorant-Binding Protein Discriminates between Sex Pheromone Components. Authors: Zhou, J.-J. / Robertson, G. / He, X. / Dufour, S. / Hooper, A.M. / Pickett, J.A. / Keep, N.H. / Field, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wch.cif.gz | 48.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wch.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 2wch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wch_validation.pdf.gz | 428.9 KB | Display | wwPDB validaton report |
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Full document | 2wch_full_validation.pdf.gz | 429.8 KB | Display | |
Data in XML | 2wch_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 2wch_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/2wch ftp://data.pdbj.org/pub/pdb/validation_reports/wc/2wch | HTTPS FTP |
-Related structure data
Related structure data | 2wc5SC 2wc6C 2wcjC 2wckC 2wclC 2wcmC 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: 16187.409 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-160 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOMBYX MORI (domestic silkworm) / Organ: ANTENNA / Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P34170 | ||||||||
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#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-B7M / ( | #4: Water | ChemComp-HOH / | Nonpolymer details | (10E,12Z)-HEXADECADI | Sequence details | THREE POINT MUTATIONS DUE TO STRAIN DIFFERENCES. THE CDNA USED FOR THIS EXPERIMENT WAS OBTAINED ...THREE POINT MUTATIONS DUE TO STRAIN DIFFERENCE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 33 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 30% PEG 4000, 200MM MGCL2, 100MM TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 30, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→43.1 Å / Num. obs: 11977 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.9 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WC5 Resolution: 1.7→43.1 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.878 / SU B: 2.496 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.148 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.45 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→43.1 Å
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Refine LS restraints |
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