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- PDB-1c02: CRYSTAL STRUCTURE OF YEAST YPD1P -

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Basic information

Entry
Database: PDB / ID: 1c02
TitleCRYSTAL STRUCTURE OF YEAST YPD1P
ComponentsPHOSPHOTRANSFERASE YPD1P
KeywordsTRANSFERASE / HELIX-BUNDLE
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 / SYNCHROTRON / Resolution: 1.8 Å
AuthorsSong, H.K. / Lee, J.Y. / Lee, M.G. / Suh, S.W.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Insights into eukaryotic multistep phosphorelay signal transduction revealed by the crystal structure of Ypd1p from Saccharomyces cerevisiae.
Authors: Song, H.K. / Lee, J.Y. / Lee, M.G. / Moon, J. / Min, K. / Yang, J.K. / Suh, S.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and preliminary X-ray analysis of Saccharomyces cerevisiae Ypd1p, a key intermediate in phosphorelay signal transduction
Authors: Lee, M.G. / Lee, J.Y. / Song, H.K. / Suh, S.W.
History
DepositionJul 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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: PHOSPHOTRANSFERASE YPD1P
B: PHOSPHOTRANSFERASE YPD1P


Theoretical massNumber of molelcules
Total (without water)38,1112
Polymers38,1112
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-8 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.013, 53.013, 244.853
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 PHOSPHOTRANSFERASE YPD1P


Mass: 19055.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: Q07688
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.36
Details: AMMONIUM SULFATE, LITHIUM SULFATE, HEPES, PEG 400, pH 7.36, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K
Crystal grow
*PLUS
Temperature: 296 K
Components of the solutions
*PLUS
Conc.: 23 mg/ml / Common name: protein

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Nov 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 319853 / Num. obs: 319853 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.279 / % possible all: 94
Reflection
*PLUS
Num. obs: 33318
Reflection shell
*PLUS
% possible obs: 94 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.247 16090 -RANDOM
Rwork0.201 ---
all0.201 32903 --
obs0.201 30518 97.6 %-
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2678 0 0 56 2734
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg0.89
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

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