+Open data
-Basic information
Entry | Database: PDB / ID: 6er7 | ||||||
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Title | CHEMOTAXIS PROTEIN CHEY FROM Pyrococcus horikoshiI | ||||||
Components | 120aa long hypothetical chemotaxis protein (CheY) | ||||||
Keywords | SIGNALING PROTEIN / SIGNAL TRANSDUCTION PROTEIN | ||||||
Function / homology | histidine phosphotransfer kinase activity / phosphorelay sensor kinase activity / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / 120aa long hypothetical chemotaxis protein (CheY) Function and homology information | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | Paithankar, K.S. / Enderle, M.E. / Wirthensohn, D. / Grininger, M. / Oesterhelt, D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2019 Title: Structure of the archaeal chemotaxis protein CheY in a domain-swapped dimeric conformation. Authors: Paithankar, K.S. / Enderle, M. / Wirthensohn, D.C. / Miller, A. / Schlesner, M. / Pfeiffer, F. / Rittner, A. / Grininger, M. / Oesterhelt, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6er7.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6er7.ent.gz | 59.2 KB | Display | PDB format |
PDBx/mmJSON format | 6er7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6er7_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 6er7_full_validation.pdf.gz | 435.8 KB | Display | |
Data in XML | 6er7_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 6er7_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/6er7 ftp://data.pdbj.org/pub/pdb/validation_reports/er/6er7 | HTTPS FTP |
-Related structure data
Related structure data | 6exrC 3tmyS 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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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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-Components
#1: Protein | Mass: 13190.697 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0482 / Production host: Escherichia coli (E. coli) / References: UniProt: O58193 |
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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: 2.9 Å3/Da / Density % sol: 58.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl 1.2 M sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→34 Å / Num. obs: 107515 / % possible obs: 99.5 % / Redundancy: 7.6 % / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.02 / Rrim(I) all: 0.03 / Net I/σ(I): 38 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TMY Resolution: 2.62→34.038 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.203 / SU B: 16.383 / SU ML: 0.315 / Cross valid method: FREE R-VALUE / ESU R: 0.564 / ESU R Free: 0.319 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.73 Å2
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Refinement step | Cycle: LAST / Resolution: 2.62→34.038 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: 20
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