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Yorodumi- PDB-1oxb: Complex between YPD1 and SLN1 response regulator domain in space ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oxb | ||||||
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Title | Complex between YPD1 and SLN1 response regulator domain in space group P2(1)2(1)2(1) | ||||||
Components |
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Keywords | SIGNALING PROTEIN / phosphorelay protein / two-component signaling protein / response regulator / HPt domain / Histidine-containing phosphotransfer protein / Ypd1p / Sln1p | ||||||
Function / homology | Function and homology information protein histidine kinase binding / osmosensor activity / transferase activity, transferring phosphorus-containing groups / histidine phosphotransfer kinase activity / osmosensory signaling via phosphorelay pathway / protein histidine kinase activity / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / cell periphery ...protein histidine kinase binding / osmosensor activity / transferase activity, transferring phosphorus-containing groups / histidine phosphotransfer kinase activity / osmosensory signaling via phosphorelay pathway / protein histidine kinase activity / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / cell periphery / phosphorylation / ATP binding / metal ion binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Xu, Q. / Porter, S.W. / West, A.H. | ||||||
Citation | Journal: Structure / Year: 2003 Title: The yeast YPD1/SLN1 complex: insights into molecular recognition in two-component signaling systems. Authors: Xu, Q. / Porter, S.W. / West, A.H. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Co-Crystallization of the Yeast Phosphorelay Protein YPD1 with the SLN1 Response-Regulator Domain and Preliminary X-ray Diffraction Analysis Authors: Chooback, L. / 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 | 1oxb.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oxb.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 1oxb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/1oxb ftp://data.pdbj.org/pub/pdb/validation_reports/ox/1oxb | HTTPS FTP |
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-Related structure data
Related structure data | 1oxkC 1qspS 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: 19056.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: YPD1 / Plasmid: pUC12 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q07688 |
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#2: Protein | Mass: 15092.516 Da / Num. of mol.: 1 / Fragment: C-terminal residues 1087-1220 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SLN1 OR YPD2 OR YIL147C / Plasmid: pCYB2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P39928, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 2.88 Å3/Da / Density % sol: 57.01 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: ammonium sulfate, sodium acetate, BeCl2, NaF, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Choobakc, L., (2003) Acta Cryst., D59, 927. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: osmic confocal mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 17288 / Num. obs: 17288 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.3→2.44 Å / % possible all: 94.5 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 17319 / Num. measured all: 84027 |
Reflection shell | *PLUS % possible obs: 94.5 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 6.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QSP (YPD1) Resolution: 2.3→30.16 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1933271.52 / Data cutoff high rms absF: 1933271.52 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.1863 Å2 / ksol: 0.383349 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→30.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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