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- PDB-1oxb: Complex between YPD1 and SLN1 response regulator domain in space ... -

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Basic information

Entry
Database: PDB / ID: 1oxb
TitleComplex between YPD1 and SLN1 response regulator domain in space group P2(1)2(1)2(1)
Components
  • SLN1
  • Ypd1p
KeywordsSIGNALING PROTEIN / phosphorelay protein / two-component signaling protein / response regulator / HPt domain / Histidine-containing phosphotransfer protein / Ypd1p / Sln1p
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / protein histidine kinase binding / osmosensor activity / histidine phosphotransfer kinase activity / protein histidine kinase activity / osmosensory signaling via phosphorelay pathway / phosphorelay sensor kinase activity / histidine kinase / phosphorelay signal transduction system / cell periphery ...transferase activity, transferring phosphorus-containing groups / protein histidine kinase binding / osmosensor activity / histidine phosphotransfer kinase activity / protein histidine kinase activity / osmosensory signaling via phosphorelay pathway / phosphorelay sensor kinase activity / histidine kinase / phosphorelay signal transduction system / cell periphery / ATP binding / metal ion binding / nucleus / plasma membrane / 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 / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain ...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 / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Osmosensing histidine protein kinase SLN1 / Phosphorelay intermediate protein YPD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXu, Q. / Porter, S.W. / West, A.H.
Citation
Journal: Structure / Year: 2003
Title: The yeast YPD1/SLN1 complex: insights into molecular recognition in two-component signaling systems.
Authors: Xu, Q. / Porter, S.W. / West, A.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Co-Crystallization of the Yeast Phosphorelay Protein YPD1 with the SLN1 Response-Regulator Domain and Preliminary X-ray Diffraction Analysis
Authors: Chooback, L. / West, A.H.
History
DepositionApr 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ypd1p
B: SLN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2453
Polymers34,1492
Non-polymers961
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-29 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.730, 74.250, 98.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ypd1p


Mass: 19056.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YPD1 / Plasmid: pUC12 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q07688
#2: Protein SLN1 / Osmolarity two-component system protein


Mass: 15092.516 Da / Num. of mol.: 1 / Fragment: C-terminal residues 1087-1220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SLN1 OR YPD2 OR YIL147C / Plasmid: pCYB2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P39928, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.88 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: ammonium sulfate, sodium acetate, BeCl2, NaF, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Choobakc, L., (2003) Acta Cryst., D59, 927.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-12 mg/mlprotein1drop
22-3 Mammonium sulfate1reservoir
350 mMsodium acetate1reservoirpH5.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: osmic confocal mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 17288 / Num. obs: 17288 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19
Reflection shellResolution: 2.3→2.44 Å / % possible all: 94.5
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 17319 / Num. measured all: 84027
Reflection shell
*PLUS
% possible obs: 94.5 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 6.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QSP (YPD1)

1qsp


Resolution: 2.3→30.16 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1933271.52 / Data cutoff high rms absF: 1933271.52 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1722 10 %RANDOM
Rwork0.214 ---
all0.239 17288 --
obs0.219 17244 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.1863 Å2 / ksol: 0.383349 e/Å3
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.19 Å20 Å20 Å2
2---0.31 Å20 Å2
3----5.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.3→30.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2291 0 5 54 2350
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.228 252 9.3 %
Rwork0.229 2471 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

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