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Open data
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Basic information
Entry | Database: PDB / ID: 1dy0 | ||||||
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Title | Murine endostatin, crystal form II | ||||||
![]() | COLLAGEN ALPHA1(XVIII) CHAIN | ||||||
![]() | ANGIOGENESIS INHIBITOR | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hohenester, E. / Sasaki, T. / Timpl, R. | ||||||
![]() | ![]() Title: Variable Zinc Coordination in Endostatin Authors: Hohenester, E. / Sasaki, T. / Mann, K. / Timpl, R. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50 KB | Display | ![]() |
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PDB format | ![]() | 34.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.4 KB | Display | ![]() |
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Full document | ![]() | 431.1 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dy1C ![]() 1koeS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | BIOLOGICAL_UNIT: MONOMER |
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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.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | N-TERMINAL APLA MUTATION | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.22 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 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: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 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: 9450 / % possible obs: 99.8 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.079 |
Reflection shell | Resolution: 2.2→2.32 Å / Rmerge(I) obs: 0.197 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 76689 |
Reflection shell | *PLUS % possible obs: 99.8 % |
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Processing
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Refinement | Method to determine structure: ![]() 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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