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- PDB-1c03: CRYSTAL STRUCTURE OF YPD1P (TRICLINIC FORM) -

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Basic information

Entry
Database: PDB / ID: 1c03
TitleCRYSTAL STRUCTURE OF YPD1P (TRICLINIC FORM)
ComponentsHYPOTHETICAL PROTEIN YDL235C
KeywordsSIGNALING PROTEIN / FOUR HELICAL BUNDLE / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / protein histidine kinase binding / cytokinin-activated signaling pathway / osmosensory signaling via phosphorelay pathway / histidine phosphotransfer kinase activity / phosphorelay signal transduction system / phosphorylation / 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: 2.3 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 1, 2017Group: Structure summary
Revision 1.4Feb 8, 2017Group: Database references
Revision 1.5Jul 7, 2021Group: Refinement description / Category: refine / Item: _refine.ls_percent_reflns_obs
Revision 1.6Feb 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

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN YDL235C
B: HYPOTHETICAL PROTEIN YDL235C
C: HYPOTHETICAL PROTEIN YDL235C
D: HYPOTHETICAL PROTEIN YDL235C


Theoretical massNumber of molelcules
Total (without water)77,3034
Polymers77,3034
Non-polymers00
Water3,171176
1
A: HYPOTHETICAL PROTEIN YDL235C


Theoretical massNumber of molelcules
Total (without water)19,3261
Polymers19,3261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HYPOTHETICAL PROTEIN YDL235C


Theoretical massNumber of molelcules
Total (without water)19,3261
Polymers19,3261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HYPOTHETICAL PROTEIN YDL235C


Theoretical massNumber of molelcules
Total (without water)19,3261
Polymers19,3261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: HYPOTHETICAL PROTEIN YDL235C


Theoretical massNumber of molelcules
Total (without water)19,3261
Polymers19,3261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.343, 66.480, 66.491
Angle α, β, γ (deg.)106.37, 106.66, 115.33
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: Protein
HYPOTHETICAL PROTEIN YDL235C / YPD1P


Mass: 19325.799 Da / Num. of mol.: 4 / Mutation: C-TERMINAL 6 HIS-TAG
Source method: isolated from a genetically manipulated source
Details: TRICLINIC FORM
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET-22B / Production host: Escherichia coli (E. coli) / References: UniProt: Q07688
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.36
Details: PEG 400, ammonium sulfate, Hepes, Li2SO4, pH 7.36, VAPOR DIFFUSION, HANGING DROP, temperature 297K
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 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 59932 / Num. obs: 59932 / % possible obs: 88.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.9
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.26 / % possible all: 85.9
Reflection
*PLUS
Num. obs: 35254
Reflection shell
*PLUS
% possible obs: 85.9 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1498 5 %Random
Rwork0.206 ---
all0.206 34106 --
obs0.206 34106 95 %-
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5220 0 0 176 5396
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg0.94

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