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Yorodumi- PDB-2qeo: Crystal Structure of Anopheles gambiae D7R4-norepinephrine complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qeo | ||||||
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Title | Crystal Structure of Anopheles gambiae D7R4-norepinephrine complex | ||||||
Components | D7R4 Protein | ||||||
Keywords | LIGAND BINDING PROTEIN / All-helical / Odorant-binding protein | ||||||
Function / homology | Function and homology information odorant binding / vasodilation / sensory perception of smell / extracellular region Similarity search - Function | ||||||
Biological species | Anopheles gambiae (African malaria mosquito) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.315 Å | ||||||
Authors | Andersen, J.F. / Mans, B.J. / Calvo, E. / Ribeiro, J.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: The Crystal Structure of D7r4, a Salivary Biogenic Amine-binding Protein from the Malaria Mosquito Anopheles gambiae Authors: Mans, B.J. / Calvo, E. / Ribeiro, J.M. / Andersen, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qeo.cif.gz | 68.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qeo.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 2qeo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qeo_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
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Full document | 2qeo_full_validation.pdf.gz | 452.9 KB | Display | |
Data in XML | 2qeo_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 2qeo_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/2qeo ftp://data.pdbj.org/pub/pdb/validation_reports/qe/2qeo | HTTPS FTP |
-Related structure data
-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: 17099.857 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anopheles gambiae (African malaria mosquito) Strain: G3 / Gene: D7r4 / Plasmid: pET17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9BIH3 #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | THERE IS CHIRALITY ISSUE AT CAL CENTER OF LIGAND LNR | |
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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: 2.45 Å3/Da / Density % sol: 49.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 30 %PEG 6000, 0.1M Tris HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.978743 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Jan 1, 2006 / Details: mirrors |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978743 Å / Relative weight: 1 |
Reflection | Resolution: 2.315→87.71 Å / Num. all: 14718 / Num. obs: 14718 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.082 / Χ2: 0.975 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.315→2.39 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1464 / Χ2: 0.647 / % possible all: 100 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.315→87.71 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.36 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.339 / ESU R Free: 0.249 / 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: 42.729 Å2
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Refinement step | Cycle: LAST / Resolution: 2.315→87.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.315→2.375 Å / Total num. of bins used: 20
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