+Open data
-Basic information
Entry | Database: PDB / ID: 4fu4 | ||||||
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Title | Human collagenase 3 (MMP-13) with peptide from pro-domain | ||||||
Components |
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Keywords | HYDROLASE / protein-peptide complex / collagenase / collagen / cleavage with MMP3 / pro-peptide / metzincin / Zinc metalloprotease / collagen cleavage | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.849 Å | ||||||
Authors | Stura, E.A. / Vera, L. / Visse, R. / Nagase, H. / Dive, V. | ||||||
Citation | Journal: Faseb J. / Year: 2013 Title: Crystal structure of full-length human collagenase 3 (MMP-13) with peptides in the active site defines exosites in the catalytic domain. Authors: Stura, E.A. / Visse, R. / Cuniasse, P. / Dive, V. / Nagase, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fu4.cif.gz | 180 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fu4.ent.gz | 141.9 KB | Display | PDB format |
PDBx/mmJSON format | 4fu4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/4fu4 ftp://data.pdbj.org/pub/pdb/validation_reports/fu/4fu4 | HTTPS FTP |
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-Related structure data
Related structure data | 4fvlC 4g0dC 1pexS 2ow9S 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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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 42284.617 Da / Num. of mol.: 2 / Fragment: Inactive full form (UNP residues 104-471) / Mutation: E223A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMP13 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Protein/peptide | Mass: 3109.209 Da / Num. of mol.: 2 / Fragment: pro-domain fragment (UNP residues 25-50) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMP13 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P45452 |
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-Non-polymers , 5 types, 146 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | AFTER CLEAVAGE WITH PROTEASE MMP3 TO CLEAVE OFF THE PRO-DOMAIN TO GIVE RISE TO THE MATURE (INACTIVE) ...AFTER CLEAVAGE WITH PROTEASE MMP3 TO CLEAVE OFF THE PRO-DOMAIN TO GIVE RISE TO THE MATURE (INACTIVE) PROTEASE (E223A), A FRAGMENT OF THE PRO-PEPTIDE IS BOUND BACK ONTO THE INACTIVE PROTEASE. THUS CHAIN C BELONGS TO CHAIN A, AND CHAIN D BELONGS TO CHAIN B. |
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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: 2.91 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | Temperature: 277 K / Method: slow cooling / pH: 7.5 Details: PROPEPTIDE IMPURITY INDUCES CRYSTALLIZATION ON COLD STORAGE CRYOPROTECTANT: 20% MPEG2K, 10% MPEG550, 10% ethylene glycol, 90mM imidazole malate, pH 6.0, SLOW COOLING, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jul 1, 2009 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.85→50 Å / Num. all: 25132 / Num. obs: 25083 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.78 % / Biso Wilson estimate: 37.228 Å2 / Rmerge(I) obs: 0.17 / Rsym value: 0.159 / Net I/σ(I): 13.88 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PEX AND 2OW9 Resolution: 2.849→49.336 Å / SU ML: 0.38 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): -3 / Phase error: 24.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.849→49.336 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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