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Yorodumi- PDB-4d7c: Monoclinic crystal form of the extracellular olfactomedin domain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d7c | ||||||
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Title | Monoclinic crystal form of the extracellular olfactomedin domain from gliomedin | ||||||
Components | GLIOMEDIN | ||||||
Keywords | SIGNALING PROTEIN / MYELIN / BETA-PROPELLER | ||||||
Function / homology | Function and homology information clustering of voltage-gated sodium channels / protein binding involved in heterotypic cell-cell adhesion / microvillus organization / collagen trimer / axon / cell surface / signal transduction / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Han, H. / Kursula, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: The Olfactomedin Domain from Gliomedin is a Beta-Propeller with Unique Structural Properties. Authors: Han, H. / Kursula, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d7c.cif.gz | 321.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d7c.ent.gz | 266.9 KB | Display | PDB format |
PDBx/mmJSON format | 4d7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/4d7c ftp://data.pdbj.org/pub/pdb/validation_reports/d7/4d7c | HTTPS FTP |
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-Related structure data
Related structure data | 4d77SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32435.500 Da / Num. of mol.: 2 / Fragment: OLFACTOMEDIN DOMAIN, UNP RESIDUES 260-543 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q80WL1 #2: Chemical | #3: 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 % sol: 40 % / Description: NONE |
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Crystal grow | Details: 100 MM SODIUM CITRATE PH 5.5, 20% PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 78451 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 12.99 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.45→1.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.3 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4D77 Resolution: 1.45→43.084 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 24.2 / 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: 1.45→43.084 Å
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Refine LS restraints |
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LS refinement shell |
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