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Yorodumi- PDB-1yn3: Crystal Structures of EAP Domains from Staphylococcus aureus Reve... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yn3 | ||||||
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Title | Crystal Structures of EAP Domains from Staphylococcus aureus Reveal an Unexpected Homology to Bacterial Superantigens | ||||||
Components | truncated cell surface protein map-w | ||||||
Keywords | TOXIN / PROTEIN BINDING / Virulence-factor / Extracellular-adherence protein / Staphylococcus | ||||||
Function / homology | MAP domain / MAP domain / MAP repeat profile. / Ubiquitin-like (UB roll) - #120 / Ubiquitin-like (UB roll) / Roll / Alpha Beta / Protein map Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 | 1yn3.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yn3.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 1yn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/1yn3 ftp://data.pdbj.org/pub/pdb/validation_reports/yn/1yn3 | HTTPS FTP |
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-Related structure data
Related structure data | 1yn4C 1yn5SC 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: 10810.184 Da / Num. of mol.: 2 / Fragment: residues 160-254 / Mutation: V253I 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: Q99QS1 #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: 2.59 Å3/Da / Density % sol: 52.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: PEG 8000, ammonium sulfate, MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. obs: 40720 / % possible obs: 88.8 % / Biso Wilson estimate: 13.9 Å2 |
Reflection shell | Resolution: 1.35→1.45 Å / % possible all: 70.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: EapH1, pdb entry 1YN5 Resolution: 1.35→29.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 546804.14 / 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: 46.4792 Å2 / ksol: 0.363177 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.35→29.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.43 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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