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Yorodumi- PDB-3zz0: Crystal structure of ribosomal elongation factor (EF)-G from Stap... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zz0 | ||||||
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Title | Crystal structure of ribosomal elongation factor (EF)-G from Staphylococcus aureus with a fusidic acid hyper-sensitivity mutation M16I | ||||||
Components | Elongation factor GEF-G | ||||||
Keywords | TRANSLATION / GTPASE / FIVE-DOMAIN STRUCTURE | ||||||
Function / homology | Function and homology information translation elongation factor activity / GTPase activity / GTP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Koripella, R.K. / Chen, Y. / Selmer, M. / Sanyal, S. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2012 Title: Mechanism of elongation factor-G-mediated fusidic acid resistance and fitness compensation in Staphylococcus aureus. Authors: Koripella, R.K. / Chen, Y. / Peisker, K. / Koh, C.S. / Selmer, M. / Sanyal, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zz0.cif.gz | 234.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zz0.ent.gz | 191.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/3zz0 ftp://data.pdbj.org/pub/pdb/validation_reports/zz/3zz0 | HTTPS FTP |
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-Related structure data
Related structure data | 3zztC 3zzuC 1fnmS C: citing same article (ref.) S: Starting model for refinement |
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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: 76681.250 Da / Num. of mol.: 2 / Mutation: M16I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: fusA, fus / Production host: Escherichia coli (E. coli) / References: UniProt: P68790 #2: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 2.65 Å3/Da / Density % sol: 54 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9538 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 6, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9538 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→46.7 Å / Num. obs: 36516 / % possible obs: 91.1 % / Observed criterion σ(I): 1.85 / Redundancy: 3.73 % / Biso Wilson estimate: 67.91 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.55 |
Reflection shell | Resolution: 2.8→3 Å / Redundancy: 3.78 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.85 / % possible all: 76.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FNM Resolution: 2.8→46.71 Å / SU ML: 0.93 / σ(F): 2.35 / Phase error: 36.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.11 Å2 / ksol: 0.3 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→46.71 Å
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Refine LS restraints |
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LS refinement shell |
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