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Yorodumi- PDB-1jod: Crystal Structure of Murine Olfactory Marker Protein in Spacegrou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jod | ||||||
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Title | Crystal Structure of Murine Olfactory Marker Protein in Spacegroup P43212 | ||||||
Components | Olfactory Marker Protein | ||||||
Keywords | SIGNALING PROTEIN / Beta Clamshell | ||||||
Function / homology | Function and homology information neurogenesis / peptide binding / sensory perception of smell / axon / neuronal cell body / signal transduction / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Smith, P. / Hunt, J.F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: The crystal structure of the olfactory marker protein at 2.3 A resolution. Authors: Smith, P.C. / Firestein, S. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jod.cif.gz | 83.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jod.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jod_validation.pdf.gz | 425.2 KB | Display | wwPDB validaton report |
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Full document | 1jod_full_validation.pdf.gz | 433.9 KB | Display | |
Data in XML | 1jod_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 1jod_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/1jod ftp://data.pdbj.org/pub/pdb/validation_reports/jo/1jod | HTTPS FTP |
-Related structure data
Related structure data | 1f35C 1jobC 1f15S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18991.777 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q64288 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CAC / #4: Water | ChemComp-HOH / | |
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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: 4.15 Å3/Da / Density % sol: 70.39 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, Zinc Acetate, Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal grow | *PLUS Method: unknown / Details: unpublished structure |
-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9785 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Apr 15, 2000 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→40 Å / Num. all: 11102 / Num. obs: 8962 / % possible obs: 80.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Biso Wilson estimate: 59.1 Å2 |
Reflection shell | Resolution: 3.2→3.31 Å / % possible all: 61.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1F15 Resolution: 3.2→40 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.31 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 10
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