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Open data
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Basic information
Entry | Database: PDB / ID: 3ba0 | ||||||
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Title | Crystal structure of full-length human MMP-12 | ||||||
![]() | Macrophage metalloelastase | ||||||
![]() | HYDROLASE / Full-length MMP-12 / hemopexin domain / catalytic domain / domain interaction. / Calcium / Extracellular matrix / Glycoprotein / Metal-binding / Metalloprotease / Polymorphism / Protease / Secreted / Zinc / Zymogen | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bertini, I. / Calderone, V. / Fragai, M. / Jaiswal, R. / Luchinat, C. / Melikian, M. / Myonas, E. / Svergun, D.I. | ||||||
![]() | ![]() Title: Evidence of reciprocal reorientation of the catalytic and hemopexin-like domains of full-length MMP-12. Authors: Bertini, I. / Calderone, V. / Fragai, M. / Jaiswal, R. / Luchinat, C. / Melikian, M. / Mylonas, E. / Svergun, D.I. #1: ![]() Title: X-ray structure of human proMMP-1: new insights into procollagenase activation and collagen binding Authors: Jozic, D. / Bourenkov, G. / Lim, N.H. / Visse, R. / Nagase, H. / Bode, W. / Maskos, K. #2: ![]() Title: Structural insight into the complex formation of latent matrix metalloproteinase 2 with tissue inhibitor of metalloproteinase 2 Authors: Morgunova, E. / Tuuttila, A. / Bergmann, U. / Tryggvason, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.6 KB | Display | ![]() |
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PDB format | ![]() | 65.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.3 KB | Display | ![]() |
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Full document | ![]() | 531.4 KB | Display | |
Data in XML | ![]() | 26.3 KB | Display | |
Data in CIF | ![]() | 34.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jxyC ![]() 1su3S ![]() 1y93S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42143.348 Da / Num. of mol.: 1 / Mutation: F171D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-HAE / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris-HCl, 30% PEG8000, 200mM acetohydroxamic acid, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Nov 25, 2006 / Details: Enhance Ultra |
Radiation | Monochromator: Enhance Ultra / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→30.7 Å / Num. all: 9308 / Num. obs: 9308 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 36.17 Å2 / Rmerge(I) obs: 0.15 / Rsym value: 0.15 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1371 / Rsym value: 0.43 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1Y93, 1SU3 Resolution: 3→30.7 Å / Cor.coef. Fo:Fc: 0.84 / Cor.coef. Fo:Fc free: 0.709 / SU B: 24.045 / SU ML: 0.462 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.595 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 5.979 Å2
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Refine analyze | Luzzati sigma a obs: 0.46 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→30.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.077 Å / Total num. of bins used: 20
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