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Yorodumi- PDB-1f4v: CRYSTAL STRUCTURE OF ACTIVATED CHEY BOUND TO THE N-TERMINUS OF FLIM -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f4v | ||||||
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Title | CRYSTAL STRUCTURE OF ACTIVATED CHEY BOUND TO THE N-TERMINUS OF FLIM | ||||||
Components |
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Keywords | SIGNALING PROTEIN / response regulator / peptide-protein complex / bacterial signal transduction / BeF3 | ||||||
Function / homology | Function and homology information bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / bacterial-type flagellum-dependent swarming motility / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation ...bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / bacterial-type flagellum-dependent swarming motility / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity / positive chemotaxis / protein acetylation / acetyltransferase activity / cytoskeletal motor activity / phosphorelay signal transduction system / chemotaxis / magnesium ion binding / signal transduction / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.22 Å | ||||||
Authors | Lee, S.Y. / Cho, H.S. / Pelton, J.G. / Yan, D. / Henderson, R.K. / King, D. / Huang, L.S. / Kustu, S. / Berry, E.A. / Wemmer, D.E. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Crystal structure of an activated response regulator bound to its target. Authors: Lee, S.Y. / Cho, H.S. / Pelton, J.G. / Yan, D. / Henderson, R.K. / King, D.S. / Huang, L. / Kustu, S. / Berry, E.A. / Wemmer, D.E. #1: Journal: J.Mol.Biol. / Year: 2000 Title: NMR Structure of Activated CheY Authors: Cho, H.S. / Lee, S.Y. / Yan, D. / Pan, X. / Parkinson, J.S. / Kustu, S. / Wemmer, D.E. / Pelton, J.G. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Beryllofluoride Mimics Phosphorylation of NtrC and other Bacterial Response Regulators Authors: Yan, D. / Cho, H.S. / Hastings, C.A. / Igo, M.M. / Lee, S.Y. / Pelton, J.G. / Stewart, V. / Wemmer, D.E. / Kustu, S. #3: Journal: J.Biol.Chem. / Year: 1991 Title: Crystal Structure of Escherichia coli CheY Refined at 1.7-A Resolution Authors: Volz, K. / Matsumura, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f4v.cif.gz | 101.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f4v.ent.gz | 78.7 KB | Display | PDB format |
PDBx/mmJSON format | 1f4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/1f4v ftp://data.pdbj.org/pub/pdb/validation_reports/f4/1f4v | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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3 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 13981.136 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / References: UniProt: P06143, UniProt: P0AE67*PLUS #2: Protein/peptide | Mass: 1689.884 Da / Num. of mol.: 3 / Fragment: N-TERMINUS / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P06974 |
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-Non-polymers , 4 types, 288 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.79 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: ammonium sulfate, glycerol, Tris, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→24.7 Å / Num. all: 121390 / Num. obs: 28982 / % possible obs: 92.9 % / Observed criterion σ(F): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.9 | |||||||||||||||||||||||||
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.318 / Num. unique all: 1314 / % possible all: 84.7 | |||||||||||||||||||||||||
Reflection | *PLUS Num. measured all: 121390 / Rmerge(I) obs: 0.08 | |||||||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 84.7 % |
-Processing
Software |
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Refinement | Resolution: 2.22→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1216673.62 / Data cutoff high rms absF: 1216673.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 55.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.22→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.22→2.36 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.217 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 55.1 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.376 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.316 |