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Yorodumi- PDB-1sra: STRUCTURE OF A NOVEL EXTRACELLULAR CA2+-BINDING MODULE IN BM-40(S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sra | ||||||
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Title | STRUCTURE OF A NOVEL EXTRACELLULAR CA2+-BINDING MODULE IN BM-40(SLASH)SPARC(SLASH)OSTEONECTIN | ||||||
Components | SPARC | ||||||
Keywords | CALCIUM-BINDING PROTEIN / EXTRACELLULAR MATRIX PROTEIN | ||||||
Function / homology | Function and homology information Scavenging by Class H Receptors / platelet alpha granule membrane / platelet alpha granule / regulation of cell morphogenesis / extracellular matrix binding / negative regulation of endothelial cell proliferation / basement membrane / ECM proteoglycans / negative regulation of angiogenesis / Nuclear signaling by ERBB4 ...Scavenging by Class H Receptors / platelet alpha granule membrane / platelet alpha granule / regulation of cell morphogenesis / extracellular matrix binding / negative regulation of endothelial cell proliferation / basement membrane / ECM proteoglycans / negative regulation of angiogenesis / Nuclear signaling by ERBB4 / endocytic vesicle lumen / collagen binding / positive regulation of endothelial cell migration / platelet alpha granule lumen / nuclear matrix / Platelet degranulation / collagen-containing extracellular matrix / intracellular membrane-bounded organelle / calcium ion binding / cell surface / extracellular space / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Hohenester, E. / Maurer, P. / Hohenadl, C. / Timpl, R. / Jansonius, J.N. / Engel, J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1996 Title: Structure of a novel extracellular Ca(2+)-binding module in BM-40. Authors: Hohenester, E. / Maurer, P. / Hohenadl, C. / Timpl, R. / Jansonius, J.N. / Engel, J. #1: Journal: J.Mol.Biol. / Year: 1995 Title: The C-Terminal Portion of Bm-40 (Sparc(Slash)Osteonectin) is an Autonomously Folding and Crystallisable Domain that Binds Calcium and Collagen Iv Authors: Maurer, P. / Hohenadl, C. / Hohenester, E. / Gohring, W. / Timpl, R. / Engel, J. #2: Journal: Faseb J. / Year: 1994 Title: The Biology of Sparc, a Protein that Modulates Cell-Matrix Interactions Authors: Lane, T.F. / Sage, E.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sra.cif.gz | 44.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sra.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 1sra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sra_validation.pdf.gz | 363.5 KB | Display | wwPDB validaton report |
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Full document | 1sra_full_validation.pdf.gz | 362.9 KB | Display | |
Data in XML | 1sra_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 1sra_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sr/1sra ftp://data.pdbj.org/pub/pdb/validation_reports/sr/1sra | 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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Atom site foot note | 1: CIS PROLINE - PRO 225 |
-Components
#1: Protein | Mass: 17940.428 Da / Num. of mol.: 1 / Fragment: CARBOXY-TERMINAL DOMAIN (RESIDUES 136 - 286) Source method: isolated from a genetically manipulated source Details: CRYSTALLIZED FROM 0.7 M K, NA-TARTRATE, PH 7.5 + 2 MM CACL2 Source: (gene. exp.) Homo sapiens (human) / Gene: HUMAN BM-40 / Organ: KIDNEY / Plasmid: BLUESCRIPT, PCIS Cell line (production host): HUMAN EMBRYONIC KIDNEY CELLS (293, ATCC CRL 1573) Gene (production host): HUMAN BM-40 / Production host: Homo sapiens (human) / References: UniProt: P09486 | ||||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | CA 303 IS A NONIDENTIF | Source details | MOLECULE_NAME: SPARC. FRAGMENT 136 - 286 PRODUCED BY PCR. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.26 % | ||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||
Crystal | *PLUS Density % sol: 61 % | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.02 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 5, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 15597 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.063 |
Reflection | *PLUS Num. measured all: 56738 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS Redundancy: 3.6 % |
-Processing
Software |
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Refinement | Resolution: 2→8 Å / σ(F): 0
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Displacement parameters | Biso mean: 24.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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