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Yorodumi- PDB-1omd: STRUCTURE OF ONCOMODULIN REFINED AT 1.85 ANGSTROMS RESOLUTION. AN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1omd | ||||||
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Title | STRUCTURE OF ONCOMODULIN REFINED AT 1.85 ANGSTROMS RESOLUTION. AN EXAMPLE OF EXTENSIVE MOLECULAR AGGREGATION VIA CA2+ | ||||||
Components | ONCOMODULIN | ||||||
Keywords | CALCIUM BINDING PROTEIN | ||||||
Function / homology | Function and homology information cuticular plate / stereocilium / ion binding / supramolecular fiber / cochlea development / response to wounding / vesicle / calcium ion binding / protein-containing complex binding / protein homodimerization activity ...cuticular plate / stereocilium / ion binding / supramolecular fiber / cochlea development / response to wounding / vesicle / calcium ion binding / protein-containing complex binding / protein homodimerization activity / protein-containing complex / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.85 Å | ||||||
Authors | Ahmed, F.R. / Przybylska, M. / Rose, D.R. / Birnbaum, G.I. / Pippy, M.E. / Macmanus, J.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1990 Title: Structure of oncomodulin refined at 1.85 A resolution. An example of extensive molecular aggregation via Ca2+. Authors: Ahmed, F.R. / Przybylska, M. / Rose, D.R. / Birnbaum, G.I. / Pippy, M.E. / MacManus, J.P. #1: Journal: J.Mol.Biol. / Year: 1988 Title: Crystallization and Preliminary Crystallographic Data for Oncomodulin Authors: Przybylska, M. / Ahmed, F.R. / Birnbaum, G.I. / Rose, D.R. #2: Journal: J.Biol.Chem. / Year: 1987 Title: A Complete Complementary DNA for the Oncodevelopmental Calcium-Binding Protein, Oncomodulin Authors: Gillen, M.F. / Banville, D. / Rutledge, R.G. / Narang, S. / Seligy, V.L. / Whitfield, J.F. / Macmanus, J.P. #3: Journal: Eur.J.Biochem. / Year: 1983 Title: The Complete Amino Acid Sequence of Oncomodulin-A Parvalbumin-Like Calcium-Binding Protein from Morris Hepatoma 5123Tc Authors: Macmanus, J.P. / Watson, D.C. / Yaguchi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1omd.cif.gz | 36.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1omd.ent.gz | 24.5 KB | Display | PDB format |
PDBx/mmJSON format | 1omd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1omd_validation.pdf.gz | 420.1 KB | Display | wwPDB validaton report |
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Full document | 1omd_full_validation.pdf.gz | 425.7 KB | Display | |
Data in XML | 1omd_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 1omd_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/1omd ftp://data.pdbj.org/pub/pdb/validation_reports/om/1omd | HTTPS FTP |
-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: 12067.064 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / References: UniProt: P02631 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | CALCIUM 135 IS INTERMOLECULAR. IT IS BONDED DIRECTLY TO THREE DIFFERENT ONCOMODULIN MOLECULES AND ...CALCIUM 135 IS INTERMOLEC | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.74 Å3/Da / Density % sol: 29.45 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5.2 / Method: vapor diffusion, hanging drop / Details: took Przybylska et al., from original paper | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.85 Å / Num. obs: 5965 / Rmerge(I) obs: 3 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.85→6 Å /
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Refinement step | Cycle: LAST / Resolution: 1.85→6 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.166 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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