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Yorodumi- PDB-3pg2: The Crystal structure of the major pilin GBS80 of Streptococcus a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pg2 | ||||||
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Title | The Crystal structure of the major pilin GBS80 of Streptococcus agalactiae 35 kDa C-terminal fragment | ||||||
Components | Cell wall surface anchor family protein | ||||||
Keywords | STRUCTURAL PROTEIN / CELL ADHESION / Ig-like fold / Major pilin / Group B Streptococcus / GBS pili / Backbone pilin / isopeptide bond / IgG-DEv fold / IgG-rev fold / CNA A type / CNA B type / GBS / GBS80 / Pilus shaft component / Isopeptide formation / Gram-positive bacterial (Group B Streptococcus) cell surface | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus agalactiae serogroup V (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.8 Å | ||||||
Authors | Vengadesan, K. / Narayana, S.V.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: A Model for Group B Streptococcus Pilus Type 1: The Structure of a 35-kDa C-Terminal Fragment of the Major Pilin GBS80. Authors: Vengadesan, K. / Ma, X. / Dwivedi, P. / 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 | 3pg2.cif.gz | 150.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pg2.ent.gz | 121.6 KB | Display | PDB format |
PDBx/mmJSON format | 3pg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pg2_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
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Full document | 3pg2_full_validation.pdf.gz | 441.3 KB | Display | |
Data in XML | 3pg2_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 3pg2_validation.cif.gz | 50.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/3pg2 ftp://data.pdbj.org/pub/pdb/validation_reports/pg/3pg2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 35137.160 Da / Num. of mol.: 2 / Fragment: unp residues 200-518 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae serogroup V (bacteria) Genus: SAG0645 / Gene: GBS80, SAG0645 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1BLue / References: UniProt: Q8E0S9 #2: Chemical | ChemComp-CA / #3: 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: 2.35 Å3/Da / Density % sol: 47.72 % |
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Crystal grow | Temperature: 295 K / pH: 5.5 Details: 25 % PEG MME 2000, 0.1 M MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 16, 2009 |
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→37.15 Å / Num. obs: 60630 / % possible obs: 99.6 % / Redundancy: 2.81 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 9.6 |
Reflection shell | Highest resolution: 1.8 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→37.15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.878 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.137 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→37.15 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2424 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
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