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Yorodumi- PDB-4h84: Crystal structure of the catalytic domain of Human MMP12 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h84 | ||||||
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Title | Crystal structure of the catalytic domain of Human MMP12 in complex with a selective carboxylate based inhibitor. | ||||||
Components | Macrophage metalloelastase | ||||||
Keywords | hydrolase/hydrolase inhibitor / selective carboxylate based MMP-12 inhibitor / METZINCIN / Zinc protease / hydrolase-hydrolase inhibitor complex | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.592 Å | ||||||
Authors | Stura, E.A. / Antoni, C. / Vera, L. / Cassar-Lajeunesse, E. / Nuti, E. / Dive, V. / Rossello, A. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2013 Title: Crystallization of bi-functional ligand protein complexes. Authors: Antoni, C. / Vera, L. / Devel, L. / Catalani, M.P. / Czarny, B. / Cassar-Lajeunesse, E. / Nuti, E. / Rossello, A. / Dive, V. / Stura, E.A. #1: Journal: J.Struct.Biol. / Year: 2013 Title: Crystallization of bi-functional ligand protein complexes. Authors: Antoni, C. / Vera, L. / Devel, L. / Catalani, M.P. / Czarny, B. / Cassar-Lajeunesse, E. / Nuti, E. / Rossello, A. / Dive, V. / Stura, E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h84.cif.gz | 98.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h84.ent.gz | 73.2 KB | Display | PDB format |
PDBx/mmJSON format | 4h84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h84_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4h84_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4h84_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 4h84_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/4h84 ftp://data.pdbj.org/pub/pdb/validation_reports/h8/4h84 | HTTPS FTP |
-Related structure data
Related structure data | 4h1qC 4h2eC 4h30SC 4h3xC 4h49C 4h76C 4h82C 4hmaC 4i03C 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17615.670 Da / Num. of mol.: 2 / Fragment: Human MMP12 catalytic domain / Mutation: F171D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HME, MMP12 / Plasmid: PET24A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P39900, macrophage elastase |
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-Non-polymers , 8 types, 303 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | ChemComp-PGO / #6: Chemical | ChemComp-PGR / | #7: Chemical | ChemComp-GOL / #8: Chemical | #9: 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: 2.12 Å3/Da / Density % sol: 42.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein: hMMP12 F171D at4 784 mico-M + 10 milli-M AHA Reservoir: 12% PEG 20K, 0.14 M imidazole malate, .0175 M NaCl Cryoprotectant: 40% C7 (C7 = 12.5 % di-ethylene glycol + 12.5 % ethylene ...Details: Protein: hMMP12 F171D at4 784 mico-M + 10 milli-M AHA Reservoir: 12% PEG 20K, 0.14 M imidazole malate, .0175 M NaCl Cryoprotectant: 40% C7 (C7 = 12.5 % di-ethylene glycol + 12.5 % ethylene glycol + 25 % 1,2-propanediol + 12.5 % DMSO + 12.5 % glycerol), 1M NaCl, 0.1 M (MMT buffer 75% acid/25% basic), 9% PEG 10.000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2012 / Details: MIRRORS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single Silicon (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.59→50 Å / Num. all: 41050 / Num. obs: 40489 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.68 % / Biso Wilson estimate: 21.449 Å2 / Rmerge(I) obs: 0.159 / Rsym value: 0.147 / Net I/σ(I): 10.64 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4H30 Resolution: 1.592→42.029 Å / SU ML: 0.15 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2.02 / σ(I): -3 / Phase error: 19.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.592→42.029 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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