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Yorodumi- PDB-6n9d: Complex of tissue inhibitor of metalloproteinases-1 (TIMP-1) muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n9d | ||||||
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Title | Complex of tissue inhibitor of metalloproteinases-1 (TIMP-1) mutant (L34G/L133P/L151C/G154A) with matrix metalloproteinase-3 catalytic domain (MMP-3cd) | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE inhibitor / tissue inhibitor of metalloproteinases / matrix metalloproteinase / HYDROLASE / HYDROLASE-HYDROLASE inhibitor complex | ||||||
Function / homology | Function and homology information regulation of integrin-mediated signaling pathway / negative regulation of metallopeptidase activity / stromelysin 1 / peptidase inhibitor activity / connective tissue replacement involved in inflammatory response wound healing / negative regulation of trophoblast cell migration / negative regulation of membrane protein ectodomain proteolysis / metalloendopeptidase inhibitor activity / cellular response to UV-A / negative regulation of catalytic activity ...regulation of integrin-mediated signaling pathway / negative regulation of metallopeptidase activity / stromelysin 1 / peptidase inhibitor activity / connective tissue replacement involved in inflammatory response wound healing / negative regulation of trophoblast cell migration / negative regulation of membrane protein ectodomain proteolysis / metalloendopeptidase inhibitor activity / cellular response to UV-A / negative regulation of catalytic activity / regulation of neuroinflammatory response / negative regulation of endopeptidase activity / cartilage development / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / Interleukin-10 signaling / response to amyloid-beta / Collagen degradation / basement membrane / collagen catabolic process / extracellular matrix disassembly / negative regulation of reactive oxygen species metabolic process / cellular response to nitric oxide / EGFR Transactivation by Gastrin / extracellular matrix / Degradation of the extracellular matrix / response to hormone / extracellular matrix organization / response to cytokine / platelet alpha granule lumen / cytokine activity / Post-translational protein phosphorylation / growth factor activity / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / response to peptide hormone / cellular response to reactive oxygen species / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / metallopeptidase activity / Platelet degranulation / peptidase activity / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / cellular response to lipopolysaccharide / protease binding / Extra-nuclear estrogen signaling / endoplasmic reticulum lumen / serine-type endopeptidase activity / innate immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å | ||||||
Authors | Raeeszadeh-Sarmazdeh, M. / Radisky, E.S. / Sankaran, B. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Directed evolution of the metalloproteinase inhibitor TIMP-1 reveals that its N- and C-terminal domains cooperate in matrix metalloproteinase recognition. Authors: Raeeszadeh-Sarmazdeh, M. / Greene, K.A. / Sankaran, B. / Downey, G.P. / Radisky, D.C. / Radisky, E.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n9d.cif.gz | 152.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n9d.ent.gz | 118.2 KB | Display | PDB format |
PDBx/mmJSON format | 6n9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/6n9d ftp://data.pdbj.org/pub/pdb/validation_reports/n9/6n9d | HTTPS FTP |
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-Related structure data
Related structure data | 6mavC 1ueaS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18595.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMP3, STMY1 / Production host: Homo sapiens (human) / References: UniProt: P08254, stromelysin 1 | ||||
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#2: Protein | Mass: 20664.709 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TIMP1, CLGI, TIMP / Production host: Homo sapiens (human) / References: UniProt: P01033 | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2 M Sodium Acetate, 0.1 M Sodium Cacodylate: HCl, pH 6.5 18 % (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→43.99 Å / Num. obs: 14162 / % possible obs: 99.99 % / Redundancy: 20.4 % / Biso Wilson estimate: 55.93 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.2469 / Rrim(I) all: 0.2531 / Net I/σ(I): 20.11 |
Reflection shell | Resolution: 2.67→2.765 Å / Redundancy: 21.1 % / Mean I/σ(I) obs: 2.16 / Num. unique obs: 1374 / CC1/2: 0.664 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UEA Resolution: 2.67→43.99 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.22 Å2 / Biso mean: 55.1126 Å2 / Biso min: 23.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.67→43.99 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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