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Yorodumi- PDB-5jd8: Crystal structure of the serine endoprotease from Yersinia pestis -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jd8 | ||||||
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Title | Crystal structure of the serine endoprotease from Yersinia pestis | ||||||
Components | Periplasmic serine peptidase DegS | ||||||
Keywords | HYDROLASE / DegS / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity Similarity search - Function | ||||||
Biological species | Yersinia pestis CO92 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Filippova, E.V. / Wawrzsak, Z. / Sandoval, J. / Skarina, T. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of the serine endoprotease from Yersinia pestis Authors: Filippova, E.V. / Wawrzsak, Z. / Sandoval, J. / Skarina, T. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jd8.cif.gz | 122.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jd8.ent.gz | 93.8 KB | Display | PDB format |
PDBx/mmJSON format | 5jd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jd8_validation.pdf.gz | 466.8 KB | Display | wwPDB validaton report |
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Full document | 5jd8_full_validation.pdf.gz | 472 KB | Display | |
Data in XML | 5jd8_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 5jd8_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/5jd8 ftp://data.pdbj.org/pub/pdb/validation_reports/jd/5jd8 | HTTPS FTP |
-Related structure data
Related structure data | 4rqyS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-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: 35354.785 Da / Num. of mol.: 1 / Fragment: UNP residues 29-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Gene: degS, AK38_3169 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: A0A0B6NK33, UniProt: A0A5P8YL96*PLUS |
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#2: Chemical | ChemComp-CXS / |
#3: Chemical | ChemComp-PEG / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% PEG 4000, 10% Isopropane, 50 mM CAPSO buffer pH 11, 0.1 M Sodium citrate pH 5.6, 5% P200 paratone-N oil |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2016 / Details: beryllium lenses |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 26479 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RQY Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.311 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.116 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→30 Å
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Refine LS restraints |
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