+Open data
-Basic information
Entry | Database: PDB / ID: 1pex | ||||||
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Title | COLLAGENASE-3 (MMP-13) C-TERMINAL HEMOPEXIN-LIKE DOMAIN | ||||||
Components | COLLAGENASE-3 | ||||||
Keywords | METALLOPROTEASE / C-TERMINAL HEMOPEXIN-LIKE DOMAIN OF MATRIX-METALLOPROTEINASE | ||||||
Function / homology | Function and homology information growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation ...growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / collagen binding / Degradation of the extracellular matrix / extracellular matrix / extracellular matrix organization / metalloendopeptidase activity / endopeptidase activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.7 Å | ||||||
Authors | Gomis-Ruth, F.X. / Gohlke, U. / Betz, M. / Knauper, V. / Murphy, G. / Lopez-Otin, C. / Bode, W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: The helping hand of collagenase-3 (MMP-13): 2.7 A crystal structure of its C-terminal haemopexin-like domain. Authors: Gomis-Ruth, F.X. / Gohlke, U. / Betz, M. / Knauper, V. / Murphy, G. / Lopez-Otin, C. / Bode, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pex.cif.gz | 55.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pex.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 1pex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pex_validation.pdf.gz | 379.7 KB | Display | wwPDB validaton report |
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Full document | 1pex_full_validation.pdf.gz | 389.3 KB | Display | |
Data in XML | 1pex_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 1pex_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/1pex ftp://data.pdbj.org/pub/pdb/validation_reports/pe/1pex | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24183.404 Da / Num. of mol.: 1 / Fragment: C-TERMINAL HEMOPEXIN-LIKE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BREAST CANCER / Description: STABLY TRANSFECTED / Organ: BREAST / Cell (production host): 1PEX CELLS Organelle (production host): PURIFIED FROM SERUM FREE CONDITIONED CELL CULTURE MEDIUM Production host: Mus musculus (house mouse) References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases | ||||
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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→26.4 Å / Num. obs: 6858 / % possible obs: 95.7 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.063 |
Reflection | *PLUS Num. measured all: 24238 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.82 Å / % possible obs: 94.9 % |
-Processing
Software |
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Refinement | Resolution: 2.7→6 Å /
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Displacement parameters | Biso mean: 42.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.319 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |