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- PDB-1slm: CRYSTAL STRUCTURE OF FIBROBLAST STROMELYSIN-1: THE C-TRUNCATED HU... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1slm | ||||||
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Title | CRYSTAL STRUCTURE OF FIBROBLAST STROMELYSIN-1: THE C-TRUNCATED HUMAN PROENZYME | ||||||
![]() | STROMELYSIN-1 | ||||||
![]() | HYDROLASE / METALLOPROTEASE / FIBROBLAST / COLLAGEN DEGRADATION | ||||||
Function / homology | ![]() stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / cellular response to nitric oxide ...stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / cellular response to nitric oxide / negative regulation of reactive oxygen species metabolic process / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cell migration / EGFR Transactivation by Gastrin / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / cellular response to amino acid stimulus / protein catabolic process / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / Extra-nuclear estrogen signaling / serine-type endopeptidase activity / innate immune response / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Becker, J.W. | ||||||
![]() | ![]() Title: Stromelysin-1: three-dimensional structure of the inhibited catalytic domain and of the C-truncated proenzyme. Authors: Becker, J.W. / Marcy, A.I. / Rokosz, L.L. / Axel, M.G. / Burbaum, J.J. / Fitzgerald, P.M. / Cameron, P.M. / Esser, C.K. / Hagmann, W.K. / Hermes, J.D. / Springer, J.P. #1: ![]() Title: The NMR Structure of the Inhibited Catalytic Domain of Human Stromelysin-1 Authors: Gooley, P.R. / O'Connell, J.F. / Marcy, A.I. / Cuca, G.C. / Salowe, S.P. / Bush, B.L. / Hermes, J.D. / Esser, C.K. / Hagmann, W.K. / Springer, J.P. / Johnson, B.A. #2: ![]() Title: Inhibition of Matrix Metalloproteinases by N-Carboxyalkyl Peptides Authors: Chapman, K.T. / Kopka, I.E. / Durette, P.L. / Esser, C.K. / Lanza, T.J. / Izquierdo-Martin, M. / Niedzwiecki, L. / Chang, B. / Harrison, R.K. / Kuo, D.W. / Lin, T.-T. / Stein, R.L. / Hagmann, W.K. #3: ![]() Title: Human Fibroblast Stromelysin Catalytic Domain: Expression, Purification, and Characterization of a C-Terminally Truncated Form Authors: Marcy, A.I. / Eiberger, L.L. / Harrison, R. / Chan, H.K. / Hutchinson, N.I. / Hagmann, W.K. / Cameron, P.M. / Boulton, D.A. / Hermes, J.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.9 KB | Display | ![]() |
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PDB format | ![]() | 55.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418.2 KB | Display | ![]() |
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Full document | ![]() | 418.9 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 15.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 28817.412 Da / Num. of mol.: 1 / Fragment: PROPEPTIDE, CATALYTIC 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: 2.69 Å3/Da / Density % sol: 54.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: HANGING DROP VAPOR DIFFUSION. 2.0 MICROLITER DROPS OF PROENZYME SOLUTION (10 MG/ML PROTEIN, 5.0 MILLIMOLAR CALCIUM CHLORIDE, 50 MICROMOLAR ZINC ACETATE, 0.02% SODIUM AZIDE, 20 MILLIMOLAR ...Details: HANGING DROP VAPOR DIFFUSION. 2.0 MICROLITER DROPS OF PROENZYME SOLUTION (10 MG/ML PROTEIN, 5.0 MILLIMOLAR CALCIUM CHLORIDE, 50 MICROMOLAR ZINC ACETATE, 0.02% SODIUM AZIDE, 20 MILLIMOLAR MES, PH 6.5, 0.02 MOLE INHIBITOR PER MOLE PROENZYME) WERE MIXED WITH AN EQUAL VOLUME OF RESERVOIR BUFFER (14% PEG-6000, 5% SATURATED SODIUM CITRATE, 0.02% SODIUM AZIDE, 0.1 M CACODYLATE, PH 5.8) AND INCUBATED AT 4 DEGREES CENTIGRADE., vapor diffusion - hanging drop, temperature 277K PH range: 5.8-6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 4, 1993 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 24169 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 2.82 % / Rmerge(I) obs: 0.0448 / Rsym value: 0.0555 / Net I/σ(I): 8.29 |
Reflection shell | Resolution: 1.9→2 Å / Mean I/σ(I) obs: 1.45 / % possible all: 95.8 |
Reflection shell | *PLUS % possible obs: 95.8 % |
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Processing
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Refinement | Resolution: 1.9→20 Å / Cross valid method: FREE-R / σ(F): 2
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Displacement parameters | Biso mean: 33.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Total num. of bins used: 20
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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