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Open data
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Basic information
Entry | Database: PDB / ID: 1qsp | ||||||
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Title | CRYSTAL STRUCTURE OF THE YEAST PHOSPHORELAY PROTEIN YPD1 | ||||||
![]() | YPD1 | ||||||
![]() | SIGNALING PROTEIN / FOUR-HELIX BUNDLE / HISTIDINE-CONTAINING PHOSPHOTRANSFER (HPT) DOMAIN / TWO- COMPONENT SIGNAL TRANSDUCTION | ||||||
Function / homology | ![]() transferase activity, transferring phosphorus-containing groups / protein histidine kinase binding / osmosensory signaling via phosphorelay pathway / histidine phosphotransfer kinase activity / phosphorelay signal transduction system / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Xu, Q. / West, A.H. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77 KB | Display | ![]() |
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PDB format | ![]() | 59.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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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.) ![]() ![]() Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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 |
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Processing
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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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |