+Open data
-Basic information
Entry | Database: PDB / ID: 3r72 | ||||||
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Title | Apis mellifera odorant binding protein 5 | ||||||
Components | Odorant binding protein ASP5 | ||||||
Keywords | TRANSPORT PROTEIN / helical protein / odorant molecules / antennae | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Apis mellifera (honey bee) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Spinelli, S. / Iovinella, I. / Lagarde, A. / Tegoni, M. / Pelosi, P. / Cambillau, C. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Apis mellifera odorant binding protein 5 Authors: Spinelli, S. / Iovinella, I. / Lagarde, A. / Tegoni, M. / Pelosi, P. / Cambillau, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r72.cif.gz | 128.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r72.ent.gz | 108.9 KB | Display | PDB format |
PDBx/mmJSON format | 3r72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r7/3r72 ftp://data.pdbj.org/pub/pdb/validation_reports/r7/3r72 | HTTPS FTP |
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-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: 14337.521 Da / Num. of mol.: 1 / Fragment: UNP residues 23-143 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Apis mellifera (honey bee) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WRW2 | ||
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#2: Chemical | #3: 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: 2.11 Å3/Da / Density % sol: 41.64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 20-25% PEG1500, MIB pH 3.7-4, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.975 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 27, 2010 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→38.13 Å / Num. all: 42573 / Num. obs: 42573 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.15→1.21 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.4 / Num. unique all: 6095 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→38.13 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.036 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.038 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 10.071 Å2
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Refine analyze | Luzzati coordinate error free: 0.036 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→38.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.18 Å / Total num. of bins used: 20
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