+Open data
-Basic information
Entry | Database: PDB / ID: 1c3i | ||||||
---|---|---|---|---|---|---|---|
Title | HUMAN STROMELYSIN-1 CATALYTIC DOMAIN COMPLEXED WITH RO-26-2812 | ||||||
Components | STROMELYSIN-1Matrix metalloproteinase | ||||||
Keywords | HYDROLASE / stromelysin-1 / site mutant (GLU202-GLN) | ||||||
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: 1.83 Å | ||||||
Authors | Steele, D.L. / Kammlott, R.U. / Crowther, R.L. / Birktoft, J.J. / Dunten, P. / Engler, J.E. | ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1c3i.cif.gz | 87.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1c3i.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 1c3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/1c3i ftp://data.pdbj.org/pub/pdb/validation_reports/c3/1c3i | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19416.529 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH SYNTHETIC INHIBITOR (RO-26-2812) BASED ON PRO-PEPTIDE SEQUENCE Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P08254, stromelysin 1 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-TR1 / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.61 % | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Jan 1, 1994 |
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: 1.83 Å / Num. all: 28276 / Num. obs: 20265 / Redundancy: 2.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.9 |
Reflection | *PLUS % possible obs: 70.6 % |
-Processing
Software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.83→20 Å /
| ||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→20 Å
| ||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||
Refine LS restraints | *PLUS
|