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- PDB-1qsp: CRYSTAL STRUCTURE OF THE YEAST PHOSPHORELAY PROTEIN YPD1 -

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Basic information

Entry
Database: PDB / ID: 1qsp
TitleCRYSTAL STRUCTURE OF THE YEAST PHOSPHORELAY PROTEIN YPD1
ComponentsYPD1
KeywordsSIGNALING PROTEIN / FOUR-HELIX BUNDLE / HISTIDINE-CONTAINING PHOSPHOTRANSFER (HPT) DOMAIN / TWO- COMPONENT SIGNAL TRANSDUCTION
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / protein histidine kinase binding / histidine phosphotransfer kinase activity / osmosensory signaling via phosphorelay pathway / phosphorelay signal transduction system / nucleus / cytoplasm
Similarity search - Function
Histidine-containing phosphotransfer protein 1-5/Phosphorelay intermediate protein YPD1 / HPT domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphorelay intermediate protein YPD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsXu, 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
DepositionJun 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YPD1
B: YPD1


Theoretical massNumber of molelcules
Total (without water)37,9392
Polymers37,9392
Non-polymers00
Water1,874104
1
A: YPD1


Theoretical massNumber of molelcules
Total (without water)18,9691
Polymers18,9691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YPD1


Theoretical massNumber of molelcules
Total (without water)18,9691
Polymers18,9691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.710, 52.710, 244.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein YPD1


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 / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-ID
130-33 %(w/v)PEG40001reservoir
20.1 Msodium acetate1reservoir
30.2 Mammonium acetate1reservoir
410-12 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 20, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
SHELXmodel building
SHARPphasing
DMmodel building
XFITdata reduction
X-PLORrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
SHELXphasing
DMphasing
RefinementResolution: 2.7→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.254 736 RANDOM
Rwork0.201 --
all0.206 9635 -
obs0.206 52152 -
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 0 104 2770
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.664
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
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

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