[English] 日本語
Yorodumi- PDB-1kth: The Anisotropic Refinement Of Kunitz Type Domain C5 at 0.95 Angstrom -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kth | ||||||
---|---|---|---|---|---|---|---|
Title | The Anisotropic Refinement Of Kunitz Type Domain C5 at 0.95 Angstrom | ||||||
Components | Collagen alpha 3(VI) chain | ||||||
Keywords | STRUCTURAL PROTEIN / ANISOTROPIC REFINEMENT / KUNITZ INHIBITOR / EXTRACELLULAR MATRIX / CONNECTIVE TISSUE | ||||||
Function / homology | Function and homology information collagen type VI trimer / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / NCAM1 interactions / muscle organ development / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / ECM proteoglycans ...collagen type VI trimer / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / NCAM1 interactions / muscle organ development / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / ECM proteoglycans / Integrin cell surface interactions / response to glucose / response to UV / phosphatidylinositol 3-kinase/protein kinase B signal transduction / extracellular matrix / serine-type endopeptidase inhibitor activity / sarcolemma / extracellular vesicle / collagen-containing extracellular matrix / neuron apoptotic process / cell adhesion / endoplasmic reticulum lumen / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.95 Å | ||||||
Authors | Arnoux, B. / Ducruix, A. / Prange, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Anisotropic behaviour of the C-terminal Kunitz-type domain of the alpha3 chain of human type VI collagen at atomic resolution (0.9 A). Authors: Arnoux, B. / Ducruix, A. / Prange, T. #1: Journal: J.Mol.Biol. / Year: 1995 Title: The 1.6 A structure of Kunitz-Type domain from the alpha 3 chain of human type VI collagen. Authors: Arnoux, B. / Merigeau, K. / Saludjian, P. / Norris, F. / Norris, K. / Bjorn, S. / Olsen, O. / Petersen, L. / Ducruix, A. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: 1.2 A Refinement of the Kunitz Type Domain from the alpha3 Chain of Human Type VI Collagen. Authors: Merigeau, K. / Arnoux, B. / Perahia, D. / Norris, K. / Norris, F. / Ducruix, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kth.cif.gz | 38.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kth.ent.gz | 25.7 KB | Display | PDB format |
PDBx/mmJSON format | 1kth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/1kth ftp://data.pdbj.org/pub/pdb/validation_reports/kt/1kth | HTTPS FTP |
---|
-Related structure data
Related structure data | 2kntS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 6639.508 Da / Num. of mol.: 1 / Fragment: Kunitz-type Domain C5, C-Terminus Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): mt-663 / References: UniProt: P12111 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.55 Å3/Da / Density % sol: 36.38 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.4 Details: phosphate buffer, sodium sulfate, pH 3.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 K / pH: 3 / Method: vapor diffusion, sitting drop / Details: Arnoux, B., (1995) J. Mol. Biol., 246, 609. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 1998 |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→8 Å / Num. all: 28107 / Num. obs: 22448 / % possible obs: 90.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 0.95→0.97 Å / Rmerge(I) obs: 0.051 / Num. unique all: 1598 / % possible all: 85.2 |
Reflection | *PLUS Highest resolution: 0.95 Å / Num. obs: 33572 / % possible obs: 95.2 % / Num. measured all: 179075 / Rmerge(I) obs: 0.041 |
Reflection shell | *PLUS Rmerge(I) obs: 0.34 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2KNT Resolution: 0.95→5 Å / Num. parameters: 5097 / Num. restraintsaints: 6007 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 551.81 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→5 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 0 / Num. reflection Rfree: 1147 / % reflection Rfree: 6 % / Rfactor all: 0.132 / Rfactor obs: 0.121 / Rfactor Rfree: 0.162 / Rfactor Rwork: 0.136 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_plane_restr / Dev ideal: 0.041 |