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Yorodumi- PDB-5dz9: Streptococcus agalactiae AgI/II polypeptide BspA C-terminal domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dz9 | ||||||
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Title | Streptococcus agalactiae AgI/II polypeptide BspA C-terminal domain (Mut) | ||||||
Components | BspA | ||||||
Keywords | CELL ADHESION / Adhesin / Streptococcus agalactiae | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus agalactiae serotype III | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Rego, S. / Till, M. / Race, P.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural and Functional Analysis of Cell Wall-anchored Polypeptide Adhesin BspA in Streptococcus agalactiae. Authors: Rego, S. / Heal, T.J. / Pidwill, G.R. / Till, M. / Robson, A. / Lamont, R.J. / Sessions, R.B. / Jenkinson, H.F. / Race, P.R. / Nobbs, A.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dz9.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dz9.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 5dz9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dz9_validation.pdf.gz | 420.5 KB | Display | wwPDB validaton report |
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Full document | 5dz9_full_validation.pdf.gz | 421.8 KB | Display | |
Data in XML | 5dz9_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 5dz9_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/5dz9 ftp://data.pdbj.org/pub/pdb/validation_reports/dz/5dz9 | HTTPS FTP |
-Related structure data
Related structure data | 5dz8C 5dzaC 2woyS S: Starting model for refinement C: citing same article (ref.) |
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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: 37094.844 Da / Num. of mol.: 1 / Fragment: UNP residues 554-881 / Mutation: G744D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae serotype III (strain NEM316) (bacteria) Gene: gbs1143 / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8E589 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M MMT buffer (1:2:2 L-Malic acid, MES, Tris-HCl pH 6.0) and 25% (w/v) PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→58.53 Å / Num. obs: 35603 / % possible obs: 99.4 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.89→1.94 Å / Rmerge(I) obs: 0.835 / Num. unique all: 2482 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WOY Resolution: 1.89→58.53 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.138 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.137 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.575 Å2
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Refinement step | Cycle: 1 / Resolution: 1.89→58.53 Å
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Refine LS restraints |
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