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Yorodumi- PDB-6ekg: Crystal structure of an archaeal CheY from Methanoccocus maripaludis -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ekg | ||||||
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Title | Crystal structure of an archaeal CheY from Methanoccocus maripaludis | ||||||
Components | Chemotaxis protein CheY | ||||||
Keywords | METAL BINDING PROTEIN / Chemotaxis / archaea / phosphorylation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methanococcus maripaludis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Altegoer, F. / Bange, G. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Structure and function of the archaeal response regulator CheY. Authors: Quax, T.E.F. / Altegoer, F. / Rossi, F. / Li, Z. / Rodriguez-Franco, M. / Kraus, F. / Bange, G. / Albers, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ekg.cif.gz | 66.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ekg.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ekg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/6ekg ftp://data.pdbj.org/pub/pdb/validation_reports/ek/6ekg | HTTPS FTP |
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-Related structure data
Related structure data | 6ekhC 1u0sS 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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Unit cell |
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-Components
#1: Protein | Mass: 13534.839 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanococcus maripaludis (archaea) / Gene: cheY, MMP0933 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6LYQ5 |
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#2: Chemical | ChemComp-MG / |
#3: 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: 2.22 Å3/Da / Density % sol: 44.72 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Magnesium formate 20 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→44.1 Å / Num. obs: 44463 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.047 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.15→1.17 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4361 / CC1/2: 0.69 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U0S Resolution: 1.15→41.544 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→41.544 Å
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Refine LS restraints |
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LS refinement shell |
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