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Yorodumi- PDB-5cfa: Crystal structures of Bbp from Staphylococcus aureus with peptide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cfa | ||||||
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Title | Crystal structures of Bbp from Staphylococcus aureus with peptide ligand | ||||||
Components |
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Keywords | PROTEIN BINDING/PEPTIDE / Bbp / Fibrinogen / Sdr / MSCRAMM / Staphylococcus aureus / PROTEIN BINDING-PEPTIDE complex | ||||||
Function / homology | Function and homology information blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane ...blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extracellular matrix structural constituent / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / positive regulation of peptide hormone secretion / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein polymerization / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of vasoconstriction / fibrinolysis / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / response to calcium ion / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by BRAF and RAF1 fusions / extracellular vesicle / Platelet degranulation / ER-Phagosome pathway / protein-containing complex assembly / collagen-containing extracellular matrix / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / blood microparticle / cell adhesion / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / innate immune response / signaling receptor binding / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Yu, Y. / Zhang, X.Y. / Gu, J.K. | ||||||
Citation | Journal: Protein Cell / Year: 2015 Title: Crystal structures of Bbp from Staphylococcus aureus reveal the ligand binding mechanism with Fibrinogen alpha Authors: Zhang, X.Y. / Wu, M. / Zhuo, W. / Gu, J.K. / Zhang, S.S. / Ge, J.P. / Yang, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cfa.cif.gz | 169.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cfa.ent.gz | 130.3 KB | Display | PDB format |
PDBx/mmJSON format | 5cfa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cfa_validation.pdf.gz | 450 KB | Display | wwPDB validaton report |
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Full document | 5cfa_full_validation.pdf.gz | 452.3 KB | Display | |
Data in XML | 5cfa_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 5cfa_validation.cif.gz | 56.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/5cfa ftp://data.pdbj.org/pub/pdb/validation_reports/cf/5cfa | HTTPS FTP |
-Related structure data
Related structure data | 5cf3SC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36500.008 Da / Num. of mol.: 2 / Fragment: UNP residues 272-598 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: bbp / Production host: Escherichia coli (E. coli) / References: UniProt: Q14U76 #2: Protein/peptide | Mass: 1666.704 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02671 #3: Chemical | ChemComp-MG / | #4: 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: 2.22 Å3/Da / Density % sol: 44.6 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: peptide was added into the concentrated protein samples at 10:1 ratio and the protein-peptide complex crystals are grown in 0.2 M lithium sulfate, 0.1M Tris-HCl pH8.2, 30% PEG4000 protein ...Details: peptide was added into the concentrated protein samples at 10:1 ratio and the protein-peptide complex crystals are grown in 0.2 M lithium sulfate, 0.1M Tris-HCl pH8.2, 30% PEG4000 protein concentration was 30mg/ml |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→50 Å / Num. obs: 116230 / % possible obs: 99.2 % / Redundancy: 5.1 % / Biso Wilson estimate: 16.76 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.041 / Rrim(I) all: 0.093 / Χ2: 1.408 / Net I/av σ(I): 26.812 / Net I/σ(I): 6.9 / Num. measured all: 591166 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CF3 Resolution: 1.45→36.56 Å / FOM work R set: 0.8246 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.31 Å2 / Biso mean: 22.46 Å2 / Biso min: 8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→36.56 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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