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Open data
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Basic information
Entry | Database: PDB / ID: 5l2d | ||||||
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Title | Streptococcal surface adhesin - CshA NR2 | ||||||
![]() | Surface-associated protein CshA | ||||||
![]() | CELL ADHESION / Streptococcus / adhesin | ||||||
Function / homology | ![]() GEVED domain / GEVED domain / CshA domain / Surface adhesin CshA, non-repetitive domain 2 / Surface adhesin CshA non-repetitive domain 2 / Surface adhesin CshA repetitive domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Back, C.R. / Race, P.R. / Jenkinson, H.F. | ||||||
![]() | ![]() Title: The Streptococcus gordonii Adhesin CshA Protein Binds Host Fibronectin via a Catch-Clamp Mechanism. Authors: Back, C.R. / Sztukowska, M.N. / Till, M. / Lamont, R.J. / Jenkinson, H.F. / Nobbs, A.H. / Race, P.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.5 KB | Display | ![]() |
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PDB format | ![]() | 84.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.6 KB | Display | ![]() |
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Full document | ![]() | 467.6 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36776.012 Da / Num. of mol.: 4 / Fragment: UNP residues 223-540 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288 Gene: cshA, SGO_0854 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() Method details: The structure of CshA-NR2 was initially determined in space group P6222, with two molecules in the asymmetric unit, to 3.5 A resolution by the single wavelength anomalous dispersion ...Method details: The structure of CshA-NR2 was initially determined in space group P6222, with two molecules in the asymmetric unit, to 3.5 A resolution by the single wavelength anomalous dispersion (SAD) method as applied to selonomethionine (SeMet) labeled crystals of dimeric CshA-NR2. Identification of heavy atom sites and the resulting initial phase calculation was carried out, employing diffraction data collected from two different crystals of SeMet labeled dimeric CshA-NR2, which were merged together. The software located 18 Se sites. The output model was refined and used as a molecular replacement search model to elucidate a higher resolution CshA-NR2 structure (2.7 A), employing diffraction data collected from a crystal of unlabeled CshA-NR2 (also in space group P6222). |
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Sample preparation
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M Na/K tartrate, MMT buffer [DL-malic acid, MES and Tris base in the molar ratios 1:2:2] (pH 5.0), 22% PEG 3350. |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→61.01 Å / Num. obs: 27284 / % possible obs: 100 % / Redundancy: 16.8 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.66→2.8 Å / Redundancy: 16.6 % / Rmerge(I) obs: 1.477 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 66.933 Å2
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Refinement step | Cycle: LAST / Resolution: 2.66→61.01 Å
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