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Yorodumi- PDB-1c8t: HUMAN STROMELYSIN-1 (E202Q) CATALYTIC DOMAIN COMPLEXED WITH RO-26-2812 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c8t | ||||||
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Title | HUMAN STROMELYSIN-1 (E202Q) CATALYTIC DOMAIN COMPLEXED WITH RO-26-2812 | ||||||
Components | STROMELYSIN-1Matrix metalloproteinase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / PROTEIN-INHIBITOR COMPLEX / MUTANT PROTEIN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / cellular response to nitric oxide ...stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / cellular response to nitric oxide / negative regulation of reactive oxygen species metabolic process / EGFR Transactivation by Gastrin / extracellular matrix / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / peptidase activity / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / cellular response to lipopolysaccharide / Extra-nuclear estrogen signaling / serine-type endopeptidase activity / innate immune response / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | ||||||
Authors | Steele, D.L. / el-Kabbani, O. / Dunten, P. / Crowther, R.L. | ||||||
Citation | Journal: Protein Eng. / Year: 2000 Title: Expression, characterization and structure determination of an active site mutant (Glu202-Gln) of mini-stromelysin-1. Authors: Steele, D.L. / El-Kabbani, O. / Dunten, P. / Windsor, L.J. / Kammlott, R.U. / Crowther, R.L. / Michoud, C. / Engler, J.A. / Birktoft, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c8t.cif.gz | 83.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c8t.ent.gz | 62.1 KB | Display | PDB format |
PDBx/mmJSON format | 1c8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/1c8t ftp://data.pdbj.org/pub/pdb/validation_reports/c8/1c8t | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18692.777 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN / Mutation: E202Q, S252P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: GIGIVAL FIBROBLASTS / Plasmid: PGEMEX-2 / Production host: Escherichia coli (E. coli) / References: UniProt: P08254, stromelysin 1 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.6 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG, potassium chloride, calcium chloride, cacodylate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / PH range low: 7 / PH range high: 6.5 | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Jan 1, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.15 Å / Num. all: 17584 / Num. obs: 15629 / Redundancy: 5.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 19 |
Reflection shell | Highest resolution: 2.15 Å |
Reflection | *PLUS % possible obs: 88.9 % |
-Processing
Software |
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Refinement | Resolution: 2.6→20 Å /
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||
Refine LS restraints | *PLUS
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