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Yorodumi- PDB-1y93: Crystal structure of the catalytic domain of human MMP12 complexe... -
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-Basic information
Entry | Database: PDB / ID: 1y93 | ||||||
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Title | Crystal structure of the catalytic domain of human MMP12 complexed with acetohydroxamic acid at atomic resolution | ||||||
Components | Macrophage metalloelastase | ||||||
Keywords | HYDROLASE / MATRIX METALLOPROTEINASE / MMP12 / ELASTASE / COMPLEX (ELASTASE-INHIBITOR) / METALLO ELASTASE / ACETOHYDROXAMIC ACID | ||||||
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: 1.03 Å | ||||||
Authors | Bertini, I. / Calderone, V. / Cosenza, M. / Fragai, M. / Lee, Y.-M. / Luchinat, C. / Mangani, S. / Terni, B. / Turano, P. | ||||||
Citation | 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. #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. #2: Journal: J.Mol.Biol. / Year: 2001 Title: Substrate specificity determinants of human macrophage elastase (MMP-12) based on the 1.1 A crystal structure Authors: Lang, R. / Kocourek, A. / Braun, M. / Tschesche, H. / Huber, R. / Bode, W. / Maskos, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y93.cif.gz | 154.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y93.ent.gz | 121.8 KB | Display | PDB format |
PDBx/mmJSON format | 1y93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/1y93 ftp://data.pdbj.org/pub/pdb/validation_reports/y9/1y93 | HTTPS FTP |
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-Related structure data
Related structure data | 1rmzSC 1ycmC 1z3jC 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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Details | The protein is monomeric in vivo and there is one molecule in the asymmetric unit. |
-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 / Production host: Escherichia coli (E. coli) / References: UniProt: P39900, macrophage elastase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-HAE / | #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: 2.2 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Tris, PEG 6000, ACETOHYDROXAMIC ACID, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.99993 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 30, 2004 / Details: double-crystal, Si(111) and Si(220) |
Radiation | Monochromator: double-crystal, Si(111) and Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99993 Å / Relative weight: 1 |
Reflection | Resolution: 1.02→48.4 Å / Num. all: 70833 / Num. obs: 70833 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 6.63 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 1.02→1.08 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.7 / Num. unique all: 8671 / Rsym value: 0.251 / % possible all: 84.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1RMZ Resolution: 1.03→13.99 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.642 / SU ML: 0.016 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.028 / ESU R Free: 0.027 / 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: 8.688 Å2
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Refine analyze | Luzzati sigma a obs: 0.016 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.03→13.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.03→1.056 Å / Total num. of bins used: 20
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