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Yorodumi- PDB-5d2b: Crystal structure of a mutated catalytic domain of Human MMP12 in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d2b | ||||||
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Title | Crystal structure of a mutated catalytic domain of Human MMP12 in complex with an hydroxamate analogue of RXP470 | ||||||
Components | Macrophage metalloelastase | ||||||
Keywords | HYDROLASE / Metzincin / Matrix Metallo Elastase / MMP12 / human / RXP470 / Macrophage / Hydroxamate based inhibitor | ||||||
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: 1.2 Å | ||||||
Authors | Rouanet-Mehouas, C. / Devel, L. / Dive, V. / Stura, E.A. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Zinc-Metalloproteinase Inhibitors: Evaluation of the Complex Role Played by the Zinc-Binding Group on Potency and Selectivity. Authors: Rouanet-Mehouas, C. / Czarny, B. / Beau, F. / Cassar-Lajeunesse, E. / Stura, E.A. / Dive, V. / Devel, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d2b.cif.gz | 94.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d2b.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 5d2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d2b_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5d2b_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5d2b_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 5d2b_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/5d2b ftp://data.pdbj.org/pub/pdb/validation_reports/d2/5d2b | HTTPS FTP |
-Related structure data
Related structure data | 5cxaC 5czmC 5d3cC 4gqlS 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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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 UNP residues 106-263 / Mutation: F171D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMP12, HME / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39900, macrophage elastase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-56O / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: Protein : hMMP12 F171D at 820 micro-M + 10 milli-M AHA + 0.708 milli-M inhibitor. Precipitant : 20% PEG4000, 0.2 M TRIS pH 9.5 Cryoprotectant : 10 % diethylene glycol + 5 % glycerol + 10 % ...Details: Protein : hMMP12 F171D at 820 micro-M + 10 milli-M AHA + 0.708 milli-M inhibitor. Precipitant : 20% PEG4000, 0.2 M TRIS pH 9.5 Cryoprotectant : 10 % diethylene glycol + 5 % glycerol + 10 % 1,2-propanediol + 5 % 1,4-dioxane + 25% PEG6000 + 0.1 M TRIS HCl pH 8.0 PH range: 8.0-9.5 / Temp details: cooled incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: N2 stream |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9184 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2015 Details: convex horizontal pre-focussing mirror (HPM) and a pair of focusing bimorph mirrors in Kirkpatrick-Baez (KB) configuration |
Radiation | Monochromator: cryogenically cooled channel-cut Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→32.453 Å / Num. all: 96966 / Num. obs: 96542 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Rsym value: 0.089 / Net I/σ(I): 8.78 |
Reflection shell | Resolution: 1.2→1.23 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 1.53 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GQL Resolution: 1.2→32.453 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 18.94 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→32.453 Å
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Refine LS restraints |
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LS refinement shell |
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