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Yorodumi- PDB-2gkg: Receiver domain from Myxococcus xanthus social motility protein FrzS -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gkg | ||||||
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Title | Receiver domain from Myxococcus xanthus social motility protein FrzS | ||||||
Components | response regulator homolog | ||||||
Keywords | SIGNALING PROTEIN / social motility / receiver domain / signalling / high resolution | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Myxococcus xanthus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Echols, N. / Fraser, J. / Merlie, J. / Zusman, D. / Alber, T. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2007 Title: An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS. Authors: Fraser, J.S. / Merlie, J.P. / Echols, N. / Weisfield, S.R. / Mignot, T. / Wemmer, D.E. / Zusman, D.R. / Alber, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gkg.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gkg.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 2gkg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/2gkg ftp://data.pdbj.org/pub/pdb/validation_reports/gk/2gkg | HTTPS FTP |
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-Related structure data
Related structure data | 2i6fC 2nt3C 2nt4C 1w25S 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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1 |
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Unit cell |
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Details | ASU contains one copy of FrzS receiver domain. The full-length protein includes a coiled-coil domain and may oligomerize. |
-Components
#1: Protein | Mass: 13686.523 Da / Num. of mol.: 1 / Fragment: receiver domain (residues 1-124) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: FrzS / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 4063845, UniProt: O68522*PLUS |
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#2: 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: 2.01 Å3/Da / Density % sol: 38.82 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: PEG 3350, NaFormate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.8856 / Wavelength: 0.8856 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2005 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1→20 Å / Num. all: 58567 / Num. obs: 58567 / % possible obs: 99.98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 28.75 |
Reflection shell | Resolution: 1→1.02 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: GUANYLATE CYCLASE RECEIVER DOMAIN (PDB CODE: 1W25) Resolution: 1→20 Å / Num. parameters: 13613 / Num. restraintsaints: 18431 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: All hydrogen atoms on protein residues were included in the final round of refinement. Positions of hydroxyl and methyl hydrogens were refined independently.
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Refine analyze | Num. disordered residues: 31 / Occupancy sum hydrogen: 947 / Occupancy sum non hydrogen: 1204.95 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→20 Å
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Refine LS restraints |
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