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Yorodumi- PDB-5tu8: Crystal structure of Staphylococcus epidermidis Aap G58-spacer-G5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tu8 | |||||||||||||||||||||||||||||||
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Title | Crystal structure of Staphylococcus epidermidis Aap G58-spacer-G513* (variant G5-spacer-variant G5) | |||||||||||||||||||||||||||||||
Components | Aap G58-spacer-G513*Keywords | PROTEIN BINDING / biofilm intercellular adhesion Staphylococcus Aap | Function / homology | Function and homology information Biological species | Staphylococcus epidermidis (bacteria) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | Authors | Shelton, C.L. / Conrady, D.G. / Herr, A.B. | Funding support | United States, 2items |
Citation | Journal: Biochem. J. / Year: 2017 | Title: Functional consequences of B-repeat sequence variation in the staphylococcal biofilm protein Aap: deciphering the assembly code. Authors: Shelton, C.L. / Conrady, D.G. / Herr, A.B. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tu8.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tu8.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 5tu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tu8_validation.pdf.gz | 436 KB | Display | wwPDB validaton report |
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Full document | 5tu8_full_validation.pdf.gz | 439.8 KB | Display | |
Data in XML | 5tu8_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 5tu8_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/5tu8 ftp://data.pdbj.org/pub/pdb/validation_reports/tu/5tu8 | HTTPS FTP |
-Related structure data
Related structure data | 5tu7C 5tu9C 4fupS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22582.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: ATCC 35984 / RP62A / Gene: aap, SERP2398 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: Q5HKE8 #2: 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: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 100 mM sodium acetate pH 5 175 mM calcium chloride 22% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→92.25 Å / Biso Wilson estimate: 48.9 Å2 / Rmerge(I) obs: 0.15 |
Reflection shell | Resolution: 2.33→2.413 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.52 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FUP Resolution: 2.33→92.25 Å / Cor.coef. Fo:Fc: 0.9146 / Cor.coef. Fo:Fc free: 0.8903 / SU R Cruickshank DPI: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.257 / SU Rfree Blow DPI: 0.206 / SU Rfree Cruickshank DPI: 0.197
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Displacement parameters | Biso mean: 50.38 Å2
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Refine analyze | Luzzati coordinate error obs: 0.281 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.33→92.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.46 Å / Total num. of bins used: 10
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