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Yorodumi- PDB-4in9: Structure of karilysin MMP-like catalytic domain in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 4in9 | ||||||
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Title | Structure of karilysin MMP-like catalytic domain in complex with inhibitory tetrapeptide SWFP | ||||||
Components |
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Keywords | HYDROLASE / matrixin / metallopeptidase / metalloprotease / hydrolytic enzyme | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / extracellular matrix / metalloendopeptidase activity / proteolysis / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Tannerella forsythia (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 Å | ||||||
Authors | Guevara, T. / Ksiazek, M. / Skottrup, P.D. / Cerda-Costa, N. / Trillo-Muyo, S. / de Diego, I. / Riise, E. / Potempa, J. / Gomis-Ruth, F.X. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Structure of the catalytic domain of the Tannerella forsythia matrix metallopeptidase karilysin in complex with a tetrapeptidic inhibitor. Authors: Guevara, T. / Ksiazek, M. / Skottrup, P.D. / Cerda-Costa, N. / Trillo-Muyo, S. / de Diego, I. / Riise, E. / Potempa, J. / Gomis-Ruth, F.X. #1: Journal: Mol.Microbiol. / Year: 2011 Title: The structure of the catalytic domain of Tannerella forsythia karilysin reveals it is a bacterial xenologue of animal matrix metalloproteinases. Authors: Cerda-Costa, N. / Guevara, T. / Karim, A.Y. / Ksiazek, M. / Nguyen, K.A. / Arolas, J.L. / Potempa, J. / Gomis-Ruth, F.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4in9.cif.gz | 88.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4in9.ent.gz | 64.9 KB | Display | PDB format |
PDBx/mmJSON format | 4in9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/4in9 ftp://data.pdbj.org/pub/pdb/validation_reports/in/4in9 | HTTPS FTP |
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-Related structure data
Related structure data | 2xs4S S: Starting model for refinement |
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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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 18703.615 Da / Num. of mol.: 1 / Fragment: UNP residues 35-200 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tannerella forsythia (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D0EM77 |
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#2: Protein/peptide | Mass: 535.591 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Synthetic peptide arising from phage-display screening Source: (synth.) synthetic construct (others) |
-Non-polymers , 5 types, 217 molecules
#3: Chemical | #4: Chemical | ChemComp-K / | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-GOL / #7: 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: 2.38 Å3/Da / Density % sol: 48.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Best crystals were obtained at 20 degrees from 1:1 microL drops with complex solution (8mg/mL in 5mM Tris HCl pH8, 5mM calcium chloride, 0.02% sodium azide) and 0.4M sodium/potassium ...Details: Best crystals were obtained at 20 degrees from 1:1 microL drops with complex solution (8mg/mL in 5mM Tris HCl pH8, 5mM calcium chloride, 0.02% sodium azide) and 0.4M sodium/potassium tartrate as reservoir solution. Crystals were cryo-protected by immersion in cryo-solution (0.32M sodium/potassium tartrate, 25%[v/v] glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2011 |
Radiation | Monochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→42.9 Å / Num. all: 26370 / Num. obs: 26344 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.55→1.59 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 2.1 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2XS4 Resolution: 1.55→42.87 Å / Cor.coef. Fo:Fc: 0.9679 / Cor.coef. Fo:Fc free: 0.9567 / SU R Cruickshank DPI: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 17.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.137 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→42.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.61 Å / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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