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Yorodumi- PDB-1yn5: Crystal Structures of EAP Domains from Staphylococcus aureus Reve... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yn5 | ||||||
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Title | Crystal Structures of EAP Domains from Staphylococcus aureus Reveal an Unexpected Homology to Bacterial Superantigens | ||||||
Components | EapH2 | ||||||
Keywords | UNKNOWN FUNCTION / Virulence factor / Toxin / Extracellular Adherence Protein / Staphylococcus aureus | ||||||
Function / homology | MAP domain / MAP domain / MAP repeat profile. / Ubiquitin-like (UB roll) - #120 / Ubiquitin-like (UB roll) / Roll / Alpha Beta / MAP domain-containing protein / MAP domain-containing protein Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Geisbrecht, B.V. / Hamaoka, B.Y. / Perman, B. / Zemla, A. / Leahy, D.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: The Crystal Structures of EAP Domains from Staphylococcus aureus Reveal an Unexpected Homology to Bacterial Superantigens. Authors: Geisbrecht, B.V. / Hamaoka, B.Y. / Perman, B. / Zemla, A. / Leahy, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yn5.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yn5.ent.gz | 37.9 KB | Display | PDB format |
PDBx/mmJSON format | 1yn5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yn5_validation.pdf.gz | 430.8 KB | Display | wwPDB validaton report |
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Full document | 1yn5_full_validation.pdf.gz | 436.1 KB | Display | |
Data in XML | 1yn5_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1yn5_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/1yn5 ftp://data.pdbj.org/pub/pdb/validation_reports/yn/1yn5 | HTTPS FTP |
-Related structure data
Related structure data | 1yn3C 1yn4SC 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11665.274 Da / Num. of mol.: 2 / Fragment: residues 42-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Plasmid: pET28 Derivative / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q99VA9, UniProt: A0A0H3JUK5*PLUS #2: 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: 2.25 Å3/Da / Density % sol: 45.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: PEG 8000, ammonium sulfate, 2,6-hexanediol, cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 9383 / % possible obs: 91.6 % / Biso Wilson estimate: 19.8 Å2 |
Reflection shell | Resolution: 2.2→2.34 Å / % possible all: 51.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: EapH1, pdb entry 1YN4 Resolution: 2.2→28.74 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 414928.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.5064 Å2 / ksol: 0.348524 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→28.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.059 / Total num. of bins used: 6
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Xplor file |
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