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Yorodumi- PDB-4jcn: Structure of ESP, serine protease from Staphylococcus epidermidis -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jcn | ||||||
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Title | Structure of ESP, serine protease from Staphylococcus epidermidis | ||||||
Components | Glutamyl endopeptidase | ||||||
Keywords | HYDROLASE / extracellular serine protease / esp / biofilm / Glutamyl endopeptidase / Protease | ||||||
Function / homology | Function and homology information glutamyl endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Staphylococcus epidermidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Krishnan, V. / Sthanam, V.L.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Secreted proteases control autolysin-mediated biofilm growth of Staphylococcus aureus Authors: Chen, C. / Krishnan, V. / Macon, K. / Manne, K. / Narayana, S.V. / Schneewind, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jcn.cif.gz | 58.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jcn.ent.gz | 41.3 KB | Display | PDB format |
PDBx/mmJSON format | 4jcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jcn_validation.pdf.gz | 423.8 KB | Display | wwPDB validaton report |
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Full document | 4jcn_full_validation.pdf.gz | 426.9 KB | Display | |
Data in XML | 4jcn_validation.xml.gz | 12 KB | Display | |
Data in CIF | 4jcn_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/4jcn ftp://data.pdbj.org/pub/pdb/validation_reports/jc/4jcn | HTTPS FTP |
-Related structure data
Related structure data | 1qy6S 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
#1: Protein | Mass: 23602.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: JK16 / ATCC 12228 / Gene: esp, gseA, SE_1543 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0Q2, glutamyl endopeptidase |
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#2: 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: 2.11 Å3/Da / Density % sol: 41.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 15, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→41.87 Å / Num. obs: 17810 / % possible obs: 97.4 % / Redundancy: 5.16 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.14 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 5.9 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QY6 Resolution: 1.8→41.86 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.633 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.122 / 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: 22.386 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→41.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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