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- PDB-5kbx: Co-crystal structure of the Saccharomyces cerevisiae histidine ph... -

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Basic information

Entry
Database: PDB / ID: 5kbx
TitleCo-crystal structure of the Saccharomyces cerevisiae histidine phosphotransfer signaling protein Ypd1 and the receiver domain of its downstream response regulator Ssk1
Components
  • Osmolarity two-component system protein SSK1
  • Phosphorelay intermediate protein YPD1
KeywordsSIGNALING PROTEIN / two-component signaling / phosphorelay / Ypd1 / Ssk1 / response regulator / histidine phosphotransfer protein / Saccharomyces cerevisiae / co-crystal / phosphotransfer
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / protein histidine kinase binding / osmosensory signaling via phosphorelay pathway / regulation of p38MAPK cascade / histidine phosphotransfer kinase activity / cellular response to acidic pH / mitogen-activated protein kinase kinase kinase binding / cellular hyperosmotic response / phosphorelay response regulator activity / protein kinase activator activity ...transferase activity, transferring phosphorus-containing groups / protein histidine kinase binding / osmosensory signaling via phosphorelay pathway / regulation of p38MAPK cascade / histidine phosphotransfer kinase activity / cellular response to acidic pH / mitogen-activated protein kinase kinase kinase binding / cellular hyperosmotic response / phosphorelay response regulator activity / protein kinase activator activity / phosphorelay signal transduction system / regulation of actin cytoskeleton organization / 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 / Response regulator receiver domain / cheY-homologous receiver 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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Osmolarity two-component system protein SSK1 / Phosphorelay intermediate protein YPD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsMenon, S.K. / West, A.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 1158319 United States
Citation
Journal: To Be Published
Title: Insights revealed by the co-crystal structure of the Saccharomyces cerevisiae histidine phosphotransfer signaling protein Ypd1 and the receiver domain of its downstream response regulator Ssk1
Authors: Menon, S.K. / Branscum, K.M. / Foster, C.A. / West, A.H.
#1: Journal: J. Mol. Biol. / Year: 2008
Title: Crystal structure of a complex between the phosphorelay protein YPD1 and the response regulator domain of SLN1 bound to a phosphoryl analog.
Authors: Zhao, X. / Copeland, D.M. / Soares, A.S. / West, A.H.
#2: Journal: Acta Crystallogr. D Biol. Crystallogr. / 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
DepositionJun 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Oct 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / computing / diffrn / entity / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_version / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_site / struct_site_gen / symmetry
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _cell.volume / _diffrn.pdbx_serial_crystal_experiment / _entity.pdbx_number_of_molecules / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _reflns_shell.number_unique_obs / _software.version / _struct_asym.entity_id / _struct_mon_prot_cis.pdbx_omega_angle / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _symmetry.space_group_name_Hall
Description: Atomic clashes / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphorelay intermediate protein YPD1
B: Osmolarity two-component system protein SSK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1117
Polymers43,6452
Non-polymers4665
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-22 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.696, 71.696, 176.389
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw

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Components

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


Mass: 19187.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: YPD1, YDL235C, D0790 / Plasmid: pUC / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q07688
#2: Protein Osmolarity two-component system protein SSK1


Mass: 24457.375 Da / Num. of mol.: 1 / Fragment: UNP residues 495-712
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: SSK1, YLR006C / Plasmid: pCYB2 vector IMPACT system / Details (production host): fusion of pET11a + pCYB2 vector / Cell (production host): Star / Production host: Escherichia coli (E. coli) / References: UniProt: Q07084
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 0.2 M lithium sulfate, 0.1 M CAPS/NaOH pH 10.5, 1.2 M NaH2PO4/0.8 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid N2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97910, 0.97930, 0.9116
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2014 / Details: Rh coated flat
RadiationMonochromator: Si(111) Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
30.91161
ReflectionResolution: 2.798→33.7 Å / Num. obs: 10695 / % possible obs: 89 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 42.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.037 / Net I/σ(I): 34
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 9.2 / Num. unique obs: 1163 / % possible all: 44

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000708data reduction
HKL-2000708data scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→33.27 Å / SU ML: 0.3645 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.5826
Details: ellipsoidal truncation was applied to the data/ overall d_min = 2.8 d_min along a*= 3.1 d_min along b*= 3.1 d_min along c*= 2.8
RfactorNum. reflection% reflection
Rfree0.2785 1061 10 %
Rwork0.2275 --
obs0.2325 10608 88.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.18 Å2
Refinement stepCycle: LAST / Resolution: 2.8→33.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 28 31 2427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00142436
X-RAY DIFFRACTIONf_angle_d0.35023276
X-RAY DIFFRACTIONf_chiral_restr0.0364372
X-RAY DIFFRACTIONf_plane_restr0.0022413
X-RAY DIFFRACTIONf_dihedral_angle_d7.98441479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.920.3688660.2667602X-RAY DIFFRACTION46.13
2.92-3.080.3267980.2679886X-RAY DIFFRACTION66.89
3.08-3.270.38311420.26891288X-RAY DIFFRACTION96.62
3.27-3.520.29541450.2531283X-RAY DIFFRACTION98.08
3.52-3.880.30971420.22641292X-RAY DIFFRACTION96.89
3.88-4.440.22941510.1951352X-RAY DIFFRACTION99.54
4.44-5.590.22231530.1971377X-RAY DIFFRACTION99.87
5.59-33.270.27111640.2351467X-RAY DIFFRACTION99.57
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)
14.86287688596-0.650378551552.223261377894.691882999290.2926225310335.439184925230.2626583439370.0413751182463-0.383681897062-0.1001249423-0.3319672600320.6288953381520.725782930999-0.823906604766-0.03306477121890.327171987192-0.104997112618-0.00854573236420.435952629428-0.06138071918780.22729480812628.15724410461.085240059361.6206112022
23.728296107142.55091372738-0.6344393294753.41362285849-0.7484106214075.104419448710.228338568074-0.02669631015410.5422172047710.205667760472-0.01548057008790.522761967685-0.430736343481-0.642161359216-0.1122550101390.2613128426230.1301783291130.05117061275750.2752199080240.01819122624260.22961485996938.443742541883.101678945748.1206140571
34.67040319611.10938895375-3.024565000160.266267719591-0.4975542121329.27577492079-0.01747105017620.51487148951.45379576278-0.140822349969-0.1144272430950.967500511706-2.120487175910.04361450792940.3147736357450.5942103562420.0105475200939-0.2953393602930.5671165693450.1512098972780.40447717246246.432093716793.607767360936.0872922181
44.9658284840.491422887892-2.125334270027.29694896436-7.208788337647.66671293489-0.1407853705461.54442260194-1.29489132545-1.875769050540.6382140527471.168723921451.89565466567-1.53564874472-0.3290934331210.650590305035-0.0144446666167-0.1346446469160.77217189046-0.2021143764090.51302164853134.647950025170.098753358637.6035416204
54.183963341462.53567499429-1.009443104782.48631068401-1.465455768761.70962929598-0.4095263905520.382985464814-0.544758920888-0.7066315295190.379002395837-0.3402735815870.8517884879330.283144616040.1020381521350.394673255430.156188025292-0.0373963843490.323820270014-0.08895052612150.16728652980449.058401231175.160936692241.9842735517
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 167 )
2X-RAY DIFFRACTION2chain 'B' and (resid 499 through 579 )
3X-RAY DIFFRACTION3chain 'B' and (resid 596 through 606 )
4X-RAY DIFFRACTION4chain 'B' and (resid 607 through 625 )
5X-RAY DIFFRACTION5chain 'B' and (resid 626 through 659 )

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