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Open data
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Basic information
Entry | Database: PDB / ID: 2oy4 | ||||||
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Title | Uninhibited human MMP-8 | ||||||
![]() | Neutrophil collagenase | ||||||
![]() | HYDROLASE / MMP-8 / Matrix Metalloproteinase | ||||||
Function / homology | ![]() neutrophil collagenase / tumor necrosis factor binding / positive regulation of microglial cell activation / positive regulation of neuroinflammatory response / positive regulation of tumor necrosis factor-mediated signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly ...neutrophil collagenase / tumor necrosis factor binding / positive regulation of microglial cell activation / positive regulation of neuroinflammatory response / positive regulation of tumor necrosis factor-mediated signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / metalloendopeptidase activity / specific granule lumen / positive regulation of tumor necrosis factor production / tertiary granule lumen / peptidase activity / cellular response to lipopolysaccharide / collagen-containing extracellular matrix / endopeptidase activity / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Calderone, V. / Bertini, I. / Fragai, M. / Luchinat, C. / Maletta, M. / Yeo, K.J. | ||||||
![]() | ![]() Title: Snapshots of the reaction mechanism of matrix metalloproteinases. Authors: Bertini, I. / Calderone, V. / Fragai, M. / Luchinat, C. / Maletta, M. / Yeo, K.J. #1: ![]() Title: Crystal structure of MMP8 complexed with HMR2909 Authors: Matter, H. / Schwab, W. / Barbier, D. / Billen, G. / Haase, B. / Neises, B. / Schudok, M. / Thorwart, W. / Schreuder, H. / Brachvogel, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.2 KB | Display | ![]() |
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PDB format | ![]() | 60.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.9 KB | Display | ![]() |
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Full document | ![]() | 441.6 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2oxuC ![]() 2oxwC ![]() 2oxzC ![]() 2oy2C ![]() 1bzsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The protein is monomeric in vivo but there are two molecules in the asymmetric unit. |
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Components
#1: Protein | Mass: 17612.115 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris-HCl, 20% PEG3350, 200mM acetohydroxamic acid, 0.2M MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 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: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→39.55 Å / Num. all: 30329 / Num. obs: 30329 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 16.14 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4603 / Rsym value: 0.245 / % possible all: 88.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1BZS Resolution: 1.7→33.17 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.886 / SU B: 3.533 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.163 / ESU R Free: 0.163 / 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: 17.176 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→33.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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