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Yorodumi- PDB-3ehx: Crystal structure of the catalytic domain of human MMP12 complexe... -
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-Basic information
Entry | Database: PDB / ID: 3ehx | ||||||
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Title | Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor (R)-2-(biphenyl-4-ylsulfonamido)-4-methylpentanoic acid | ||||||
Components | Macrophage metalloelastase | ||||||
Keywords | HYDROLASE / MATRIX METALLOPROTEINASE / MMP12 / ELASTASE / COMPLEX (ELASTASE-INHIBITOR) / METALLO ELASTASE / Calcium / Extracellular matrix / Glycoprotein / Metal-binding / Metalloprotease / Polymorphism / Protease / Secreted / Zinc / Zymogen | ||||||
Function / homology | Function and homology information macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development ...macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / positive regulation of interferon-alpha production / core promoter sequence-specific DNA binding / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / cellular response to virus / metalloendopeptidase activity / protein import into nucleus / endopeptidase activity / sequence-specific DNA binding / serine-type endopeptidase activity / calcium ion binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Calderone, V. | ||||||
Citation | Journal: Bioconjug.Chem. / Year: 2009 Title: Biotin-tagged probes for MMP expression and activation: design, synthesis, and binding properties Authors: Dragoni, E. / Calderone, V. / Fragai, M. / Jaiswal, R. / Luchinat, C. / Nativi, C. #1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2003 Title: X-ray structures of binary and ternary enzyme-product-inhibitor complexes of matrix metalloproteinases Authors: Bertini, I. / Calderone, V. / Fragai, M. / Luchinat, C. / Mangani, S. / Terni, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ehx.cif.gz | 52 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ehx.ent.gz | 34.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ehx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ehx_validation.pdf.gz | 705.8 KB | Display | wwPDB validaton report |
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Full document | 3ehx_full_validation.pdf.gz | 706.8 KB | Display | |
Data in XML | 3ehx_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 3ehx_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/3ehx ftp://data.pdbj.org/pub/pdb/validation_reports/eh/3ehx | HTTPS FTP |
-Related structure data
Related structure data | 3ehyC 1y93S C: citing same article (ref.) S: Starting model for refinement |
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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: 17484.475 Da / Num. of mol.: 1 / Fragment: Catalytic domain, UNP residues 106-263 / Mutation: F171D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: HME / Gene: MMP12 / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P39900, macrophage elastase | ||||||
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#2: Chemical | #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: 2.17 Å3/Da / Density % sol: 43.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris, 30% PEG 8000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54056 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Apr 1, 2008 / Details: Mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30.275 Å / Num. all: 11585 / Num. obs: 11585 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 9.1 / Num. unique all: 1553 / Rsym value: 0.169 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Y93 Resolution: 1.9→30.275 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.078 / SU ML: 0.089 / Isotropic thermal model: Isotropic (metals anisotropic) / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.172 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.04 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30.275 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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