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Yorodumi- PDB-3wgk: STAPHYLOCOCCUS AUREUS FTSZ T7 mutant substituted for GAG, DeltaT7... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wgk | ||||||
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Title | STAPHYLOCOCCUS AUREUS FTSZ T7 mutant substituted for GAG, DeltaT7GAG-GDP | ||||||
Components | Cell division protein FtsZ | ||||||
Keywords | CELL CYCLE / FTSZ / GTP-BINDING / TUBULIN HOMOLOG / POLYMERIZATION / GTPase / CELL DIVISION | ||||||
Function / homology | Function and homology information chloroplast fission / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / GTPase activity / GTP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.799 Å | ||||||
Authors | Han, X. / Matsui, T. / Yu, J. / Tanaka, I. / Yao, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structural change in FtsZ Induced by intermolecular interactions between bound GTP and the T7 loop Authors: Matsui, T. / Han, X. / Yu, J. / Yao, M. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wgk.cif.gz | 123.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wgk.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 3wgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/3wgk ftp://data.pdbj.org/pub/pdb/validation_reports/wg/3wgk | HTTPS FTP |
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-Related structure data
Related structure data | 3wgjC 3wglC 3wgmC 3wgnC 2vxyS 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: 40972.711 Da / Num. of mol.: 2 / Mutation: 204SGEVN208 to GAG Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: ftsZ / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A029 #2: Chemical | Sequence details | UNP RESIDUES 204-208 (SGEVN) WERE REPLACED WITH GAG. | |
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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: 1.84 Å3/Da / Density % sol: 33.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Sodium Acetate, 0.1M Tris-HCl, 30%(w/v) PEG4000, vapor diffusion, sitting drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 4, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.799→50 Å / Num. obs: 14645 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 83.82 Å2 / Rmerge(I) obs: 0.093 / Χ2: 4.859 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VXY Resolution: 2.799→37.446 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.772 / SU ML: 0.36 / σ(F): 1.39 / Phase error: 29.34 / 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: 125.53 Å2 / Biso mean: 76.0253 Å2 / Biso min: 33.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.799→37.446 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: 8
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