+Open data
-Basic information
Entry | Database: PDB / ID: 2oxu | ||||||
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Title | Uninhibited form of human MMP-12 | ||||||
Components | Macrophage metalloelastase | ||||||
Keywords | HYDROLASE / MMP-12 / Matrix Metalloproteinase | ||||||
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 / positive regulation of interferon-alpha production / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / core promoter sequence-specific DNA binding / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / cellular response to virus / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å | ||||||
Authors | Calderone, V. / Bertini, I. / Fragai, M. / Luchinat, C. / Maletta, M. / Yeo, K.J. | ||||||
Citation | Journal: ANGEW.CHEM.INT.ED.ENGL. / Year: 2006 Title: Snapshots of the reaction mechanism of matrix metalloproteinases. Authors: Bertini, I. / Calderone, V. / Fragai, M. / Luchinat, C. / Maletta, M. / Yeo, K.J. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Conformational variability of matrix metalloproteinases: Beyond a single 3D structure. Authors: Bertini, I. / Calderone, V. / Cosenza, M. / Fragai, M. / Lee, Y.-M. / Luchinat, C. / Mangani, S. / Terni, B. / Turano, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oxu.cif.gz | 85.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oxu.ent.gz | 62.5 KB | Display | PDB format |
PDBx/mmJSON format | 2oxu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/2oxu ftp://data.pdbj.org/pub/pdb/validation_reports/ox/2oxu | HTTPS FTP |
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-Related structure data
Related structure data | 2oxwC 2oxzC 2oy2C 2oy4C 1y93S 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: 17615.670 Da / Num. of mol.: 1 / Fragment: Catalytic Domain / Mutation: F171D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMP12, HME / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P39900, macrophage elastase | ||||
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#2: Chemical | #3: Chemical | #4: 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: 43.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Tris-HCl, 30% PEG6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.8423 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 18, 2006 Details: Fixed exit double crystal Si [111], horizontally focussing |
Radiation | Monochromator: Fixed exit double crystal Si [111], horizontally focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8423 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→19.63 Å / Num. all: 41969 / Num. obs: 41969 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 7.17 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 1.24→1.3 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 5.1 / Num. unique all: 5315 / Rsym value: 0.126 / % possible all: 84.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1Y93 Resolution: 1.24→19.64 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.924 / SU B: 1.422 / SU ML: 0.03 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.061 / ESU R Free: 0.055 / 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: 10.993 Å2
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Refinement step | Cycle: LAST / Resolution: 1.24→19.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.243→1.275 Å / Total num. of bins used: 20
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