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Yorodumi- PDB-6hhe: Crystal structure of the medfly Odorant Binding Protein CcapOBP22... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hhe | ||||||
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Title | Crystal structure of the medfly Odorant Binding Protein CcapOBP22/CcapOBP69a | ||||||
Components | Odorant binding protein OBP69a | ||||||
Keywords | TRANSPORT PROTEIN / Odorant Binding Proteins / OBP / pheromone / insect olfaction | ||||||
Function / homology | Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / Odorant binding protein OBP69a Function and homology information | ||||||
Biological species | Ceratitis capitata (Mediterranean fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.516 Å | ||||||
Authors | Falchetto, M. / Ciossani, G. / Nenci, S. / Mattevi, A. / Gasperi, G. / Forneris, F. | ||||||
Citation | Journal: Insect Mol.Biol. / Year: 2019 Title: Structural and biochemical evaluation of Ceratitis capitata odorant-binding protein 22 affinity for odorants involved in intersex communication. Authors: Falchetto, M. / Ciossani, G. / Scolari, F. / Di Cosimo, A. / Nenci, S. / Field, L.M. / Mattevi, A. / Zhou, J.J. / Gasperi, G. / Forneris, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hhe.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hhe.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 6hhe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/6hhe ftp://data.pdbj.org/pub/pdb/validation_reports/hh/6hhe | HTTPS FTP |
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-Related structure data
Related structure data | 3ognS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13833.013 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ceratitis capitata (Mediterranean fruit fly) Gene: OBP69a / Plasmid: pJexpress414 Details (production host): N-terminal 8xHis + Prescission cleavage site Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8W3V2 | ||||
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#2: Chemical | #3: Chemical | ChemComp-PG0 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.09 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES pH 6.5, 1.6 M Ammonium Sulfate, 10% v/v 1,4-Dioxane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.516→43.03 Å / Num. obs: 20882 / % possible obs: 100 % / Redundancy: 7.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.031 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.516→1.54 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.45 / Num. unique obs: 1017 / CC1/2: 0.924 / Rpim(I) all: 0.241 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OGN Resolution: 1.516→41.036 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.55 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.516→41.036 Å
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Refine LS restraints |
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LS refinement shell |
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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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