+Open data
-Basic information
Entry | Database: PDB / ID: 1qsp | ||||||
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Title | CRYSTAL STRUCTURE OF THE YEAST PHOSPHORELAY PROTEIN YPD1 | ||||||
Components | YPD1 | ||||||
Keywords | SIGNALING PROTEIN / FOUR-HELIX BUNDLE / HISTIDINE-CONTAINING PHOSPHOTRANSFER (HPT) DOMAIN / TWO- COMPONENT SIGNAL TRANSDUCTION | ||||||
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 / Resolution: 2.7 Å | ||||||
Authors | Xu, Q. / West, A.H. | ||||||
Citation | 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. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Purification, Crystallization and Preliminary X-ray Diffraction Analysis of the Yeast Phosphorelay Protein YPD1 Authors: Xu, Q. / 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 | 1qsp.cif.gz | 77 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qsp.ent.gz | 59.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qsp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/1qsp ftp://data.pdbj.org/pub/pdb/validation_reports/qs/1qsp | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18969.379 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: Q07688 #2: Water | ChemComp-HOH / | |
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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: 2.23 Å3/Da / Density % sol: 44.93 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 4000, SODIUM ACETATE AMMONIUM ACETATE, BETA-MERCAPTOETHANOL, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||
Crystal grow | *PLUS Details: Xu, Q., (1999) Acta Crystallogr., Sect.D, 55, 291. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 20, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 9674 / Num. obs: 52152 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 27.752 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.078 / % possible all: 82 |
Reflection | *PLUS Num. all: 52152 / Num. obs: 9674 |
Reflection shell | *PLUS % possible obs: 82 % / Mean I/σ(I) obs: 11.2 |
-Processing
Software |
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Refinement | Resolution: 2.7→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 30 Å / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.681 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_bond_d / Dev ideal: 0.007 |