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- PDB-6m7w: Role of the highly conserved G68 residue in the yeast phosphorela... -

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Basic information

Entry
Database: PDB / ID: 6m7w
TitleRole of the highly conserved G68 residue in the yeast phosphorelay protein Ypd1: implications for interactions between histidine phosphotransfer (HPt) and response regulator proteins
ComponentsPhosphorelay intermediate protein YPD1
KeywordsTRANSFERASE / G68Q mutant / HPt / yeast phosphorelay
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 / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsMenon, S.K. / Soni, K.S. / West, A.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 1158319 United States
Citation
Journal: BMC Biochem. / Year: 2019
Title: Role of the highly conserved G68 residue in the yeast phosphorelay protein Ypd1: implications for interactions between histidine phosphotransfer (HPt) and response regulator proteins.
Authors: Kennedy, E.N. / Hebdon, S.D. / Menon, S.K. / Foster, C.A. / Copeland, D.M. / Xu, Q. / Janiak-Spens, F. / West, A.H.
#1: Journal: Mol. Microbiol. / Year: 2000
Title: Functional roles of conserved amino acid residues surrounding the phosphorylatable histidine of the yeast phosphorelay protein YPD1.
Authors: Janiak-Spens, F. / West, A.H.
#2: 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.
#3: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 1999
Title: Purification, crystallization and preliminary X-ray diffraction analysis of the yeast phosphorelay protein YPD1.
Authors: Xu, Q. / Nguyen, V. / West, A.H.
History
DepositionAug 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Phosphorelay intermediate protein YPD1


Theoretical massNumber of molelcules
Total (without water)19,2591
Polymers19,2591
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.724, 76.724, 66.788
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Phosphorelay intermediate protein YPD1 / Histidine-containing phosphotransfer protein YPD1 / Tyrosine phosphatase-dependent protein 1


Mass: 19258.730 Da / Num. of mol.: 1 / Mutation: G68Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YPD1, YDL235C, D0790 / Plasmid: pME43 (Ypd1G68Q) / Details (production host): modified pUC12 vector / Production host: Escherichia coli (E. coli) / Strain (production host): Dh5a / References: UniProt: Q07688
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium acetate (pH 5.0), 0.2M ammonium acetate and 25-30% PEG 4000
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liq N2
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 17, 2015 / Details: Varimax HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 15936 / % possible obs: 97 % / Redundancy: 6.3 % / Biso Wilson estimate: 23.73 Å2 / CC1/2: 0.879 / Rmerge(I) obs: 0.051 / Net I/σ(I): 31
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.95 / Num. unique all: 1400 / % possible all: 72

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QSP

1qsp


Resolution: 1.98→47.104 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2074 1486 9.96 %
Rwork0.1783 --
obs0.1813 14924 92.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→47.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1344 0 0 166 1510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011383
X-RAY DIFFRACTIONf_angle_d11869
X-RAY DIFFRACTIONf_dihedral_angle_d23.376535
X-RAY DIFFRACTIONf_chiral_restr0.358214
X-RAY DIFFRACTIONf_plane_restr0.006245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9796-2.04350.2825950.2303946X-RAY DIFFRACTION71
2.0435-2.11650.26991300.20881126X-RAY DIFFRACTION86
2.1165-2.20130.23611150.22011057X-RAY DIFFRACTION81
2.2013-2.30150.30411320.25441193X-RAY DIFFRACTION92
2.3015-2.42280.24781350.19441192X-RAY DIFFRACTION91
2.4228-2.57460.23131420.17351293X-RAY DIFFRACTION97
2.5746-2.77330.20761440.17751293X-RAY DIFFRACTION98
2.7733-3.05240.20371440.17691295X-RAY DIFFRACTION98
3.0524-3.4940.1881470.16481310X-RAY DIFFRACTION98
3.494-4.40150.16861500.14711325X-RAY DIFFRACTION99
4.4015-47.11780.1841520.17111408X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.97310.9596-1.08074.7235-0.78483.2127-0.04210.17130.4014-0.02320.02290.0791-0.2393-0.0130.02150.1139-0.0318-0.04680.1595-0.01190.1626-33.71926.00092.7816
25.25243.7378-3.30948.7288-5.47918.7848-0.00710.1478-0.04780.3511-0.01280.8033-0.2163-0.8604-0.00430.16980.01790.04890.2122-0.07880.2359-44.800816.96375.7651
33.30042.3818-0.39554.6555-0.59853.3643-0.04710.2983-0.3783-0.0758-0.02890.20570.2996-0.17860.07460.1606-0.0256-0.01240.1283-0.0610.1782-35.96879.53540.5978
47.62740.5779-0.97644.03361.89987.39940.0244-0.5911-0.0530.5298-0.2868-0.8163-0.13171.6420.25380.29480.0096-0.09830.38790.06080.3676-24.025312.56159.7151
57.56184.8459-3.94398.9692-0.91612.83170.1638-1.0431-1.43050.808-0.34311.13721.3887-0.59520.18420.7517-0.15320.08650.41420.05990.7442-46.3103-3.539113.2047
63.91784.133-1.099.7126-1.17192.55160.1631-0.18450.05760.2476-0.1831-0.144-0.08440.27580.02740.1112-0.02030.0090.1513-0.01270.1112-30.654217.86997.2024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 73 )
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 105 )
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 125 )
5X-RAY DIFFRACTION5chain 'A' and (resid 126 through 134 )
6X-RAY DIFFRACTION6chain 'A' and (resid 135 through 167 )

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