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Yorodumi- PDB-456c: CRYSTAL STRUCTURE OF COLLAGENASE-3 (MMP-13) COMPLEXED TO A DIPHEN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 456c | ||||||
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Title | CRYSTAL STRUCTURE OF COLLAGENASE-3 (MMP-13) COMPLEXED TO A DIPHENYL-ETHER SULPHONE BASED HYDROXAMIC ACID | ||||||
Components | MMP-13 | ||||||
Keywords | MATRIX METALLOPROTEASE / HYDROLASE | ||||||
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 organization / extracellular matrix / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Lovejoy, B. / Welch, A. / Carr, S. / Luong, C. / Broka, C. / Hendricks, R.T. / Campbell, J. / Walker, K. / Martin, R. / Van Wart, H. / Browner, M.F. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Crystal structures of MMP-1 and -13 reveal the structural basis for selectivity of collagenase inhibitors. Authors: Lovejoy, B. / Welch, A.R. / Carr, S. / Luong, C. / Broka, C. / Hendricks, R.T. / Campbell, J.A. / Walker, K.A. / Martin, R. / Van Wart, H. / Browner, M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 456c.cif.gz | 95 KB | Display | PDBx/mmCIF format |
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PDB format | pdb456c.ent.gz | 72.7 KB | Display | PDB format |
PDBx/mmJSON format | 456c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 456c_validation.pdf.gz | 528.5 KB | Display | wwPDB validaton report |
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Full document | 456c_full_validation.pdf.gz | 537.3 KB | Display | |
Data in XML | 456c_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 456c_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/56/456c ftp://data.pdbj.org/pub/pdb/validation_reports/56/456c | HTTPS FTP |
-Related structure data
Related structure data | 830cC 966cC 1cgfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18909.076 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 110-269 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: CDNA CONSTRUCT / Production host: Escherichia coli (E. coli) References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.37 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1996 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. obs: 12287 / % possible obs: 90.6 % / Observed criterion σ(I): 0.5 / Redundancy: 3.26 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 6.9 / % possible all: 85.3 |
Reflection | *PLUS Rmerge(I) obs: 0.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CGF Resolution: 2.4→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0.5
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Displacement parameters | Biso mean: 13.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.5 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.209 / Rfactor Rfree: 0.334 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS % reflection Rfree: 7.2819 % |