+Open data
-Basic information
Entry | Database: PDB / ID: 3zq3 | ||||||
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Title | Crystal Structure of Rat Odorant Binding Protein 3 (OBP3) | ||||||
Components | OBP3 PROTEIN | ||||||
Keywords | ODORANT BINDING PROTEIN / LIPOCALIN / ENTHALPY-ENTROPY | ||||||
Function / homology | Function and homology information pheromone binding / odorant binding / small molecule binding / extracellular region Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Portman, K.L. / Long, J. / Carr, S. / Brand, L. / Winzor, D.J. / Searle, M. / Scott, D.J. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Enthalpy/Entropy Compensation Effects from Cavity Desolvation Underpin Broad Ligand Binding Selectivity for Rat Odorant Binding Protein 3 Authors: Portman, K.L. / Long, J. / Carr, S. / Briand, L. / Winzor, D.J. / Searle, M.S. / Scott, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zq3.cif.gz | 136.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zq3.ent.gz | 107.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zq3_validation.pdf.gz | 449.1 KB | Display | wwPDB validaton report |
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Full document | 3zq3_full_validation.pdf.gz | 450.6 KB | Display | |
Data in XML | 3zq3_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 3zq3_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/3zq3 ftp://data.pdbj.org/pub/pdb/validation_reports/zq/3zq3 | HTTPS FTP |
-Related structure data
Related structure data | 2a2uS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 20 - 178 / Label seq-ID: 14 - 172
NCS ensembles :
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-Components
#1: Protein | Mass: 19939.244 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PQE31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q78E14, UniProt: Q63213*PLUS |
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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: 2.64 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.02 M D-GLUCOSE, 0.02 M D-GALACTOSE, 0.02 M L-FUCOSE, 0.02M D-XYLOSE, 0.02M N-ACETYL-D-GLUCOSAMINE, 0.1 M MORPHEUS BUFFER 1 PH 6.5, 10 % W/V POLYETHYLENE GLYCOL, 20 % POLYETHYLENE GLYCOL 550 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2012 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→67.8 Å / Num. obs: 19952 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.8 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2A2U Resolution: 2.8→67.776 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.876 / SU B: 14.313 / SU ML: 0.279 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.376 / 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 / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.566 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→67.776 Å
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Refine LS restraints |
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