+Open data
-Basic information
Entry | Database: PDB / ID: 1dy1 | ||||||
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Title | Murine endostatin, crystal form III | ||||||
Components | COLLAGEN ALPHA1(XVIII) CHAIN | ||||||
Keywords | ANGIOGENESIS INHIBITOR | ||||||
Function / homology | Function and homology information vascular endothelial cell proliferation / Activation of Matrix Metalloproteinases / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / blood vessel endothelial cell migration / Integrin cell surface interactions / notochord development / extracellular matrix structural constituent conferring tensile strength ...vascular endothelial cell proliferation / Activation of Matrix Metalloproteinases / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / blood vessel endothelial cell migration / Integrin cell surface interactions / notochord development / extracellular matrix structural constituent conferring tensile strength / endothelial cell morphogenesis / collagen trimer / positive regulation of endothelial cell apoptotic process / endothelial cell apoptotic process / collagen fibril organization / positive regulation of vascular endothelial cell proliferation / basement membrane / positive regulation of blood vessel endothelial cell migration / extracellular matrix organization / skeletal system development / angiogenesis / collagen-containing extracellular matrix / cell adhesion / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Hohenester, E. / Sasaki, T. / Timpl, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Variable Zinc Coordination in Endostatin Authors: Hohenester, E. / Sasaki, T. / Mann, K. / Timpl, R. #1: Journal: Embo J. / Year: 1998 Title: Crystal Structure of the Angiogenesis Inhibitor Endostatin at 1.5 Angstrom Resolution Authors: Hohenester, E. / Sasaki, T. / Olsen, B.R. / Timpl, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dy1.cif.gz | 50.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dy1.ent.gz | 34.6 KB | Display | PDB format |
PDBx/mmJSON format | 1dy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dy1_validation.pdf.gz | 425.6 KB | Display | wwPDB validaton report |
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Full document | 1dy1_full_validation.pdf.gz | 426.7 KB | Display | |
Data in XML | 1dy1_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 1dy1_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/1dy1 ftp://data.pdbj.org/pub/pdb/validation_reports/dy/1dy1 | HTTPS FTP |
-Related structure data
Related structure data | 1dy0C 1koeS 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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1 |
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Unit cell |
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Details | BIOLOGICAL_UNIT: MONOMER |
-Components
#1: Protein | Mass: 20753.387 Da / Num. of mol.: 1 / Fragment: ENDOSTATIN DOMAIN / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell (production host): EMBRYONIC KIDNEY CELL / Cell line (production host): EBNA-293 / Production host: HOMO SAPIENS (human) / References: UniProt: P39061 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | N-TERMINAL APLA MUTATION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.53 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1998 |
Radiation | Monochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. obs: 9988 / % possible obs: 99.3 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.106 |
Reflection shell | Resolution: 2.2→2.32 Å / Rmerge(I) obs: 0.289 / % possible all: 97.7 |
Reflection | *PLUS Num. measured all: 72598 |
Reflection shell | *PLUS % possible obs: 97.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KOE Resolution: 2.2→8 Å / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |