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Yorodumi- PDB-4es8: Crystal Structure of the adhesin domain of Epf from Streptococcus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4es8 | ||||||
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Title | Crystal Structure of the adhesin domain of Epf from Streptococcus pyogenes in P212121 | ||||||
Components | Epf | ||||||
Keywords | CELL ADHESION / carbohydrate-binding module / fibronectin-like domain / adhesin / extracellular | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.58 Å | ||||||
Authors | Linke, C. / Siemens, N. / Kreikemeyer, B. / Baker, E.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: The Extracellular Protein Factor Epf from Streptococcus pyogenes Is a Cell Surface Adhesin That Binds to Cells through an N-terminal Domain Containing a Carbohydrate-binding Module. Authors: Linke, C. / Siemens, N. / Oehmcke, S. / Radjainia, M. / Law, R.H. / Whisstock, J.C. / Baker, E.N. / Kreikemeyer, B. #1: Journal: To be Published Title: Purification, crystallization and preliminary crystallographic analysis of the adhesion domain of Epf from Streptococcus pyogenes Authors: Linke, C. / Siemens, N. / Middleditch, M. / Kreikenmeyer, B. / Baker, E.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4es8.cif.gz | 160.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4es8.ent.gz | 123.3 KB | Display | PDB format |
PDBx/mmJSON format | 4es8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4es8_validation.pdf.gz | 449.1 KB | Display | wwPDB validaton report |
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Full document | 4es8_full_validation.pdf.gz | 449.9 KB | Display | |
Data in XML | 4es8_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 4es8_validation.cif.gz | 52.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/4es8 ftp://data.pdbj.org/pub/pdb/validation_reports/es/4es8 | 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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35799.207 Da / Num. of mol.: 2 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: M49 591 / Gene: SpyoM01000212 / Plasmid: pASK_IBA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3BY62*PLUS |
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-Non-polymers , 5 types, 983 molecules
#2: Chemical | ChemComp-GOL / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-K / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 25 % (w/v) PEG3350, 400 mM K Acetate, pH 7.4, 0.02 MG/ML CHYMOTRYPSIN (Type VII, TLCK-treated, Sigma-Aldrich), temperature 291K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979420, 0.95369, 0.97941 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2001 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.579→19.803 Å / Num. all: 83319 / Num. obs: 83319 / % possible obs: 98.7 % / Redundancy: 20.4 % / Rsym value: 0.07 / Net I/σ(I): 35.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.58→19.8 Å / Cor.coef. Fo:Fc: 0.9615 / Cor.coef. Fo:Fc free: 0.9497 / Occupancy max: 1 / Occupancy min: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso max: 106.55 Å2 / Biso mean: 17.1438 Å2 / Biso min: 3.44 Å2
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Refine analyze | Luzzati coordinate error obs: 0.139 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→19.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.62 Å / Total num. of bins used: 20
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