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Yorodumi- PDB-3rbi: The Type III Crystal Structure of Streptococcus agalactiae Sortase C1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rbi | ||||||
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Title | The Type III Crystal Structure of Streptococcus agalactiae Sortase C1 | ||||||
Components | Sortase family protein | ||||||
Keywords | HYDROLASE / Sortase fold / Beta-barrel / Class C sortase / Pili biogenesis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus agalactiae serogroup V (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Khare, B. / Narayana, S.V.L. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Structural differences between the Streptococcus agalactiae housekeeping and pilus-specific sortases: SrtA and SrtC1. Authors: Khare, B. / Krishnan, V. / Rajashankar, K.R. / I-Hsiu, H. / Xin, M. / Ton-That, H. / Narayana, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rbi.cif.gz | 88 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rbi.ent.gz | 67.7 KB | Display | PDB format |
PDBx/mmJSON format | 3rbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rbi_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 3rbi_full_validation.pdf.gz | 462.2 KB | Display | |
Data in XML | 3rbi_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 3rbi_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/3rbi ftp://data.pdbj.org/pub/pdb/validation_reports/rb/3rbi | HTTPS FTP |
-Related 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 25775.227 Da / Num. of mol.: 2 / Fragment: UNP residues 43-260 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae serogroup V (bacteria) Strain: SAG 2603V/R / Gene: SAG0647, srtC1 (SAG0647) / Production host: Escherichia coli (E. coli) / Strain (production host): XL1Blue / References: UniProt: Q8E0S7 #2: Chemical | ChemComp-SO4 / #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: 2.76 Å3/Da / Density % sol: 55.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6 M ammonium sulfate, 100 mM calcium chloride, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 11, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→65.22 Å / Num. all: 12057 / Num. obs: 12026 / % possible obs: 99.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 4.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→65.22 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.842 / SU B: 16.633 / SU ML: 0.31 / Cross valid method: THROUGHOUT / ESU R Free: 0.475 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 52.346 Å2
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Refinement step | Cycle: LAST / Resolution: 3→65.22 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: 1377 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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