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Yorodumi- PDB-6poo: Novel structure of the N-terminal helical domain of BibA, a group... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6poo | ||||||
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Title | Novel structure of the N-terminal helical domain of BibA, a group B streptococcus immunogenic bacterial adhesin | ||||||
Components | BibA | ||||||
Keywords | IMMUNE SYSTEM / BibA / immunogenic / bacteria / adhesin / group B streptococcus | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus agalactiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.03 Å | ||||||
Authors | Manne, K. / Narayana, S.V. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Novel structure of the N-terminal helical domain of BibA, a group B streptococcus immunogenic bacterial adhesin. Authors: Manne, K. / Chattopadhyay, D. / Agarwal, V. / Blom, A.M. / Khare, B. / Chakravarthy, S. / Chang, C. / Ton-That, H. / Narayana, S.V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6poo.cif.gz | 62.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6poo.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 6poo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6poo_validation.pdf.gz | 398.4 KB | Display | wwPDB validaton report |
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Full document | 6poo_full_validation.pdf.gz | 401.2 KB | Display | |
Data in XML | 6poo_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 6poo_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/6poo ftp://data.pdbj.org/pub/pdb/validation_reports/po/6poo | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30970.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: gbs2018 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0E798, UniProt: Q8DWZ6*PLUS |
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Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.96 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.0, 0.2 M Magnesium Chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97959 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 29, 2017 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97959 Å / Relative weight: 1 |
Reflection | Resolution: 3.03→49.85 Å / Num. obs: 7702 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.02811 / Rrim(I) all: 0.03976 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 3.03→3.138 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1893 / Mean I/σ(I) obs: 3.46 / Num. unique obs: 737 / CC1/2: 0.905 / Rrim(I) all: 0.2678 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.03→49.844 Å / SU ML: 0.43 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 23.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.03→49.844 Å
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Refine LS restraints |
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LS refinement shell |
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