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- PDB-4ijo: Unraveling hidden allosteric regulatory sites in structurally hom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ijo | ||||||
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Title | Unraveling hidden allosteric regulatory sites in structurally homologues metalloproteases | ||||||
![]() | Macrophage metalloelastase | ||||||
![]() | HYDROLASE / Matrix Metalloproteinase / Degradation of the extracellular matrix proteins / Amphiphols / regulatory sites / Extracellular | ||||||
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 | ![]() ![]() | ||||||
![]() | Udi, Y. / Fragai, M. / Grossman, M. / Mitternacht, S. / Arad-Yellin, R. / Calderone, V. / Melikian, M. / Toccafondi, M. / Berezovsky, I.N. / Luchinat, C. / Sagi, I. | ||||||
![]() | ![]() Title: Unraveling hidden regulatory sites in structurally homologous metalloproteases Authors: Udi, Y. / Fragai, M. / Grossman, M. / Mitternacht, S. / Arad-Yellin, R. / Calderone, V. / Melikian, M. / Toccafondi, M. / Berezovsky, I.N. / Luchinat, C. / Sagi, I. #1: ![]() Title: Snapshots of the reaction mechanism of matrix metalloproteinases Authors: Bertini, I. / Calderone, V. / Fragai, M. / Luchinat, C. / Maletta, M. / Yeo, K.J. #2: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.6 KB | Display | ![]() |
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PDB format | ![]() | 33.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.5 KB | Display | ![]() |
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Full document | ![]() | 428.5 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1y93S S: Starting model for refinement |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 17484.475 Da / Num. of mol.: 1 / Fragment: UNP residues 106-263 / Mutation: F171D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Tris-HCl, 30% PEG 6000, 200mM AHA, 1.0M LiCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Mar 24, 2010 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25.6 Å / Num. all: 10933 / Num. obs: 10933 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 16.26 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2 / Num. unique all: 1043 / Rsym value: 0.392 / % possible all: 71.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1Y93 Resolution: 1.9→25.6 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / Isotropic thermal model: Isotropic, Metals anisotropic. / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.17 / 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: 19.477 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→25.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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