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Yorodumi- PDB-6m7w: Role of the highly conserved G68 residue in the yeast phosphorela... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m7w | ||||||
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Title | Role of the highly conserved G68 residue in the yeast phosphorelay protein Ypd1: implications for interactions between histidine phosphotransfer (HPt) and response regulator proteins | ||||||
Components | Phosphorelay intermediate protein YPD1 | ||||||
Keywords | TRANSFERASE / G68Q mutant / HPt / yeast phosphorelay | ||||||
Function / homology | Function and homology information protein histidine kinase binding / transferase activity, transferring phosphorus-containing groups / histidine phosphotransfer kinase activity / osmosensory signaling via phosphorelay pathway / phosphorelay signal transduction system / phosphorylation / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Menon, S.K. / Soni, K.S. / West, A.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: BMC Biochem. / Year: 2019 Title: Role of the highly conserved G68 residue in the yeast phosphorelay protein Ypd1: implications for interactions between histidine phosphotransfer (HPt) and response regulator proteins. Authors: Kennedy, E.N. / Hebdon, S.D. / Menon, S.K. / Foster, C.A. / Copeland, D.M. / Xu, Q. / Janiak-Spens, F. / West, A.H. #1: Journal: Mol. Microbiol. / Year: 2000 Title: Functional roles of conserved amino acid residues surrounding the phosphorylatable histidine of the yeast phosphorelay protein YPD1. Authors: Janiak-Spens, F. / West, A.H. #2: Journal: J. Mol. Biol. / Year: 1999 Title: Conservation of structure and function among histidine-containing phosphotransfer (HPt) domains as revealed by the crystal structure of YPD1. Authors: Xu, Q. / West, A.H. #3: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 1999 Title: Purification, crystallization and preliminary X-ray diffraction analysis of the yeast phosphorelay protein YPD1. Authors: Xu, Q. / Nguyen, V. / West, A.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m7w.cif.gz | 87 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m7w.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 6m7w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/6m7w ftp://data.pdbj.org/pub/pdb/validation_reports/m7/6m7w | HTTPS FTP |
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-Related structure data
Related structure data | 1qspS 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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-Components
#1: Protein | Mass: 19258.730 Da / Num. of mol.: 1 / Mutation: G68Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: YPD1, YDL235C, D0790 / Plasmid: pME43 (Ypd1G68Q) / Details (production host): modified pUC12 vector / Production host: Escherichia coli (E. coli) / Strain (production host): Dh5a / References: UniProt: Q07688 |
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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: 3.02 Å3/Da / Density % sol: 59.3 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M sodium acetate (pH 5.0), 0.2M ammonium acetate and 25-30% PEG 4000 Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Liq N2 |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 17, 2015 / Details: Varimax HR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. obs: 15936 / % possible obs: 97 % / Redundancy: 6.3 % / Biso Wilson estimate: 23.73 Å2 / CC1/2: 0.879 / Rmerge(I) obs: 0.051 / Net I/σ(I): 31 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.95 / Num. unique all: 1400 / % possible all: 72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QSP Resolution: 1.98→47.104 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.35 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→47.104 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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