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

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Basic information

Entry
Database: PDB / ID: 1oxk
TitleComplex between YPD1 and SLN1 response regulator domain in space group P3(2)
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


protein histidine kinase binding / osmosensor activity / transferase activity, transferring phosphorus-containing groups / histidine phosphotransfer kinase activity / osmosensory signaling via phosphorelay pathway / protein histidine kinase activity / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / cell periphery ...protein histidine kinase binding / osmosensor activity / transferase activity, transferring phosphorus-containing groups / histidine phosphotransfer kinase activity / osmosensory signaling via phosphorelay pathway / protein histidine kinase activity / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / cell periphery / phosphorylation / 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, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / 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: 2.1 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 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Ypd1p
B: SLN1
C: Ypd1p
D: SLN1
E: Ypd1p
F: SLN1
G: Ypd1p
H: SLN1
I: Ypd1p
J: SLN1
K: Ypd1p
L: SLN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,62330
Polymers204,89412
Non-polymers1,72918
Water3,729207
1
A: Ypd1p
B: SLN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4375
Polymers34,1492
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-51 kcal/mol
Surface area12990 Å2
MethodPISA, PQS
2
C: Ypd1p
D: SLN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4375
Polymers34,1492
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-43 kcal/mol
Surface area13060 Å2
MethodPISA, PQS
3
E: Ypd1p
F: SLN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4375
Polymers34,1492
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-58 kcal/mol
Surface area13140 Å2
MethodPISA, PQS
4
G: Ypd1p
H: SLN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4375
Polymers34,1492
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-42 kcal/mol
Surface area13050 Å2
MethodPISA, PQS
5
I: Ypd1p
J: SLN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4375
Polymers34,1492
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-50 kcal/mol
Surface area13100 Å2
MethodPISA, PQS
6
K: Ypd1p
L: SLN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4375
Polymers34,1492
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-57 kcal/mol
Surface area13300 Å2
MethodPISA, PQS
7
I: Ypd1p
J: SLN1
hetero molecules

A: Ypd1p
B: SLN1
C: Ypd1p
D: SLN1
E: Ypd1p
F: SLN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,74920
Polymers136,5968
Non-polymers1,15312
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation2_664-y+1,x-y+1,z-1/31
identity operation1_555x,y,z1
Buried area28200 Å2
ΔGint-444 kcal/mol
Surface area62450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.300, 91.300, 200.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
51I
61K
12B
22D
32F
42H
52J
62L

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 2

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA2 - 1671 - 166
21LEULEUCC2 - 1671 - 166
31LEULEUEE2 - 1671 - 166
41LEULEUGG2 - 1671 - 166
51LEULEUII2 - 1671 - 166
61LEULEUKK2 - 1671 - 166
12GLNGLNBB1087 - 12141 - 128
22GLNGLNDD1087 - 12141 - 128
32GLNGLNFF1087 - 12141 - 128
42GLNGLNHH1087 - 12141 - 128
52GLNGLNJJ1087 - 12141 - 128
62GLNGLNLL1087 - 12141 - 128

NCS ensembles :
ID
1
2

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Components

#1: Protein
Ypd1p


Mass: 19056.457 Da / Num. of mol.: 6 / Fragment: YPD1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YPD1 / Plasmid: pUC 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.: 6 / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.53 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: ammonium sulfate, sodium acetate, BeCl2, NaF, MnCl2, 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: 2.1→30 Å / Num. all: 104211 / Num. obs: 104211 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 30.7
Reflection shellResolution: 2.1→2.18 Å / % possible all: 72.1
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 104137 / Num. measured all: 539449
Reflection shell
*PLUS
% possible obs: 72.1 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 6.4

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QSP

1qsp


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.893 / SU B: 9.925 / SU ML: 0.271 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.284 / ESU R Free: 0.208 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25828 5221 5 %RANDOM
Rwork0.23621 ---
all0.236 104211 --
obs0.23733 98990 95.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.428 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å20 Å2
2---0.26 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13326 0 90 207 13623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02213566
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212530
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.97118291
X-RAY DIFFRACTIONr_angle_other_deg0.944329235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.15731680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.259152604
X-RAY DIFFRACTIONr_chiral_restr0.1020.22129
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214836
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022484
X-RAY DIFFRACTIONr_nbd_refined0.2470.33312
X-RAY DIFFRACTIONr_nbd_other0.2140.312225
X-RAY DIFFRACTIONr_nbtor_other0.1910.58
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.5517
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.120.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.360
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3170.3166
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.517
X-RAY DIFFRACTIONr_mcbond_it0.8921.58448
X-RAY DIFFRACTIONr_mcangle_it1.636213560
X-RAY DIFFRACTIONr_scbond_it2.37935118
X-RAY DIFFRACTIONr_scangle_it3.964.54731
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A919tight positional0.070.05
11B919tight positional0.060.05
12C919tight positional0.070.05
11D919tight positional0.060.05
13E919tight positional0.060.05
11F919tight positional0.060.05
22A2673tight positional0.040.05
21B2673tight positional0.040.05
22C2673tight positional0.040.05
22D2673tight positional0.030.05
22E2673tight positional0.030.05
23F2673tight positional0.040.05
11A1486medium positional0.080.5
11B1486medium positional0.080.5
12C1486medium positional0.080.5
11D1486medium positional0.080.5
13E1486medium positional0.080.5
11F1486medium positional0.070.5
22A1486medium positional0.010.5
21B1486medium positional0.010.5
22C1486medium positional0.010.5
22D1486medium positional0.010.5
22E1486medium positional0.010.5
23F1486medium positional0.010.5
11A919tight thermal0.170.5
11B919tight thermal0.170.5
12C919tight thermal0.170.5
11D919tight thermal0.180.5
13E919tight thermal0.170.5
11F919tight thermal0.180.5
22A2673tight thermal0.650.5
21B2673tight thermal0.630.5
22C2673tight thermal0.630.5
22D2673tight thermal0.660.5
22E2673tight thermal0.630.5
23F2673tight thermal0.660.5
11A1486medium thermal0.682
11B1486medium thermal0.72
12C1486medium thermal0.672
11D1486medium thermal0.732
13E1486medium thermal0.662
11F1486medium thermal0.672
22A1486medium thermal1.692
21B1486medium thermal1.712
22C1486medium thermal1.672
22D1486medium thermal1.752
22E1486medium thermal1.662
23F1486medium thermal1.672
LS refinement shellResolution: 2.1→2.18 Å / Num. reflection Rwork: 5317 / Total num. of bins used: 20
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.73

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