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- PDB-1jk3: Crystal structure of human MMP-12 (Macrophage Elastase) at true a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jk3 | ||||||
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Title | Crystal structure of human MMP-12 (Macrophage Elastase) at true atomic resolution | ||||||
![]() | MACROPHAGE METALLOELASTASE | ||||||
![]() | HYDROLASE / Matrix metalloproteinase / batimastat / bb94 / hydroxamic acid / MMP12 / elastase / complex (elastase-inhibitor) / metallo elastase | ||||||
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 / positive regulation of interferon-alpha production / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / core promoter sequence-specific DNA binding / collagen binding / Degradation of the extracellular matrix / extracellular matrix / extracellular matrix organization / 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 | ![]() ![]() ![]() | ||||||
![]() | Lang, R. / Kocourek, A. / Braun, M. / Tschesche, H. / Huber, R. / Bode, W. / Maskos, K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.4 KB | Display | ![]() |
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PDB format | ![]() | 66.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ueaS 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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1 |
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 17458.525 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: E219A Source method: isolated from a genetically manipulated source Details: complexed with Batimastat (BB94), residue BAT / Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-BAT / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.66 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: LiCl, MES, pH 6.4, VAPOR DIFFUSION, SITTING DROP at 273K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 10, 2000 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0503 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→22.36 Å / Num. obs: 60360 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.063 / Net I/σ(I): 12.68 |
Reflection shell | Resolution: 1.09→1.13 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.256 / % possible all: 91.9 |
Reflection | *PLUS Num. measured all: 359642 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 91.9 % / Rmerge(I) obs: 0.256 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UEA Resolution: 1.09→22.36 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.1 / SU ML: 0.029 / SU Rfree: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 11.976 Å2
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Refinement step | Cycle: LAST / Resolution: 1.09→22.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.091→1.12 Å / Total num. of bins used: 20
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |