+Open data
-Basic information
Entry | Database: PDB / ID: 1itv | ||||||
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Title | Dimeric form of the haemopexin domain of MMP9 | ||||||
Components | MMP9 | ||||||
Keywords | HYDROLASE / MMP9 / adaptive molecular recognition / beta propeller / dimer | ||||||
Function / homology | Function and homology information gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / positive regulation of epidermal growth factor receptor signaling pathway / Activation of Matrix Metalloproteinases ...gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / positive regulation of epidermal growth factor receptor signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / positive regulation of release of cytochrome c from mitochondria / response to amyloid-beta / macrophage differentiation / Collagen degradation / EPH-ephrin mediated repulsion of cells / collagen catabolic process / extracellular matrix disassembly / ephrin receptor signaling pathway / positive regulation of DNA binding / negative regulation of intrinsic apoptotic signaling pathway / embryo implantation / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to cadmium ion / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of receptor binding / skeletal system development / Signaling by SCF-KIT / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / cell migration / tertiary granule lumen / peptidase activity / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / cellular response to lipopolysaccharide / ficolin-1-rich granule lumen / Extra-nuclear estrogen signaling / positive regulation of protein phosphorylation / positive regulation of apoptotic process / serine-type endopeptidase activity / apoptotic process / Neutrophil degranulation / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.95 Å | ||||||
Authors | Cha, H. / Kopetzki, E. / Huber, R. / Lanzendoerfer, M. / Brandstetter, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Structural basis of the adaptive molecular recognition by MMP9. Authors: Cha, H. / Kopetzki, E. / Huber, R. / Lanzendorfer, M. / Brandstetter, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1itv.cif.gz | 94 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1itv.ent.gz | 71.8 KB | Display | PDB format |
PDBx/mmJSON format | 1itv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/1itv ftp://data.pdbj.org/pub/pdb/validation_reports/it/1itv | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | the asu forms the biological dimer |
-Components
#1: Protein | Mass: 22450.525 Da / Num. of mol.: 2 / Fragment: haemopexin-like domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P14780, gelatinase B #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.82 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Tris, PEGMME, ammonium sulphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 3, 2001 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 1.95→20 Å / Num. all: 213889 / Num. obs: 36949 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.082 | |||||||||
Reflection shell | Resolution: 1.95→20 Å / % possible all: 97.8 | |||||||||
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 124981 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.95→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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