+Open data
-Basic information
Entry | Database: PDB / ID: 5h6i | ||||||
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Title | Crystal Structure of GBS CAMP Factor | ||||||
Components | Protein B | ||||||
Keywords | TOXIN / Pore forming toxin | ||||||
Function / homology | CAMP factor / CAMP factor (Cfa) / IgG binding / extracellular region / Protein B Function and homology information | ||||||
Biological species | Streptococcus agalactiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å | ||||||
Authors | Jin, T.C. / Brefo-Mensah, E.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2018 Title: Crystal structure of theStreptococcus agalactiaeCAMP factor provides insights into its membrane-permeabilizing activity. Authors: Jin, T. / Brefo-Mensah, E. / Fan, W. / Zeng, W. / Li, Y. / Zhang, Y. / Palmer, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h6i.cif.gz | 135 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h6i.ent.gz | 105.8 KB | Display | PDB format |
PDBx/mmJSON format | 5h6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/5h6i ftp://data.pdbj.org/pub/pdb/validation_reports/h6/5h6i | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27037.498 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P09879 #2: Chemical | #3: Chemical | ChemComp-CL / | #4: 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: 2.37 Å3/Da / Density % sol: 48.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2M NH4NO3, 20% PEG 3350, 0.1 M MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 22, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 54560 / % possible obs: 99.6 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.45→2.6 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 2.34 / CC1/2: 0.784 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.45→48.917 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→48.917 Å
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Refine LS restraints |
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LS refinement shell |
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