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- PDB-5wtb: Complex Structure of Staphylococcus aureus SdrE with human comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wtb | ||||||
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Title | Complex Structure of Staphylococcus aureus SdrE with human complement factor H | ||||||
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![]() | CELL ADHESION / Staphylococcus aureus / Sdr family / complement factor H / complement evasion | ||||||
Function / homology | ![]() regulation of complement activation, alternative pathway / symbiont cell surface / complement component C3b binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation / Regulation of Complement cascade ...regulation of complement activation, alternative pathway / symbiont cell surface / complement component C3b binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / heparin binding / blood microparticle / cell adhesion / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, M. / Zhang, Y. / Hang, T. / Wang, C. / Yang, Y. / Zang, J. / Zhang, M. / Zhang, X. | ||||||
![]() | ![]() Title: Staphylococcus aureus SdrE captures complement factor H's C-terminus via a novel 'close, dock, lock and latch' mechanism for complement evasion Authors: Zhang, Y. / Wu, M. / Hang, T. / Wang, C. / Yang, Y. / Pan, W. / Zang, J. / Zhang, M. / Zhang, X. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266.9 KB | Display | ![]() |
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PDB format | ![]() | 215 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 495.2 KB | Display | ![]() |
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Full document | ![]() | 529 KB | Display | |
Data in XML | ![]() | 48.1 KB | Display | |
Data in CIF | ![]() | 65.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5wtaC ![]() 1r17S C: citing same article ( S: Starting model for refinement |
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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: 37694.152 Da / Num. of mol.: 4 / Fragment: ligand binding A-domain, UNP residues 270-599 / Mutation: I489M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Mu50 / ATCC 700699 / Gene: sdrE, SAV0563 / Plasmid: pET22b / Production host: ![]() ![]() #2: Protein/peptide | Mass: 2511.836 Da / Num. of mol.: 4 / Fragment: UNP residues 1206-1226 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1M HEPES sodium pH 7.5, 0.2M Magnesium chloride, 30% PEG 400 (v/v) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9779 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→49.79 Å / Num. obs: 31291 / % possible obs: 96.1 % / Redundancy: 2.8 % / Rsym value: 0.1 / Net I/σ(I): 7 |
Reflection shell | Resolution: 3.3→3.48 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.9 / Num. measured obs: 4613 / Rsym value: 0.56 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1R17 Resolution: 3.3→49.79 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.886 / Cross valid method: THROUGHOUT / ESU R Free: 0.568 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.516 Å2
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Refinement step | Cycle: 1 / Resolution: 3.3→49.79 Å
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Refine LS restraints |
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