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- PDB-6lki: Two-component system protein mediate signal transduction -

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Basic information

Entry
Database: PDB / ID: 6lki
TitleTwo-component system protein mediate signal transduction
Components
  • ABC transporter, solute-binding protein
  • Sensor protein kinase HptS
KeywordsSIGNALING PROTEIN/TRANSFERASE / two-component system / G6P sensor / signal transduction / SIGNALING PROTEIN / SIGNALING PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


thiamine binding / thiamine transport / thiamine pyrophosphate binding / phosphorelay sensor kinase activity / histidine kinase / outer membrane-bounded periplasmic space / signal transduction / ATP binding / plasma membrane
Similarity search - Function
Signal transduction histidine kinase, internal region / : / Histidine kinase / Bacterial extracellular solute-binding protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Periplasmic binding protein-like II / Histidine kinase/HSP90-like ATPase superfamily / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONIC ACID / Sensor protein kinase HptS / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.781 Å
AuthorsWang, M. / Tao, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Interface switch mediates signal transmission in a two-component system.
Authors: Wang, M. / Guo, Q. / Zhu, K. / Fang, B. / Yang, Y. / Teng, M. / Li, X. / Tao, Y.
History
DepositionDec 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 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: ABC transporter, solute-binding protein
B: Sensor protein kinase HptS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4473
Polymers54,3432
Non-polymers1041
Water5,567309
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-9 kcal/mol
Surface area21790 Å2
Unit cell
Length a, b, c (Å)95.231, 106.642, 120.331
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-678-

HOH

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Components

#1: Protein ABC transporter, solute-binding protein / Extracellular solute-binding protein / Iron ABC transporter substrate-binding protein / Lipoprotein ...Extracellular solute-binding protein / Iron ABC transporter substrate-binding protein / Lipoprotein / Periplasmic-iron-binding protein BitC


Mass: 33898.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: E4U00_07700, EP54_06205, EQ90_12025, HMPREF3211_02751, NCTC10654_00249, NCTC10702_00414, RK64_01575
Production host: Escherichia coli (E. coli) / References: UniProt: X5DVD1
#2: Protein Sensor protein kinase HptS


Mass: 20444.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / Gene: hptS, SAOUHSC_00185 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2G1E0, histidine kinase
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 60% v/v Tacsimate pH 7.0, 0.1 M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 57600 / % possible obs: 98.1 % / Redundancy: 12.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.053 / Rrim(I) all: 0.185 / Net I/σ(I): 15.83
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.274 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 4922 / CC1/2: 0.779 / Rpim(I) all: 0.419 / Rrim(I) all: 1.345 / % possible all: 85.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.781→48.749 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 1999 3.47 %
Rwork0.2095 55565 -
obs0.2104 57564 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.07 Å2 / Biso mean: 43.9828 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 1.781→48.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 7 309 4126
Biso mean--39.82 43.85 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023910
X-RAY DIFFRACTIONf_angle_d0.4865289
X-RAY DIFFRACTIONf_chiral_restr0.043580
X-RAY DIFFRACTIONf_plane_restr0.003687
X-RAY DIFFRACTIONf_dihedral_angle_d4.5562373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7811-1.82560.37781180.3717327582
1.8256-1.8750.36261370.3411381695
1.875-1.93010.33251430.3104398599
1.9301-1.99240.33551430.27513993100
1.9924-2.06360.27291440.25673996100
2.0636-2.14630.24081440.22874005100
2.1463-2.2440.23171460.22154035100
2.244-2.36230.23231440.21414026100
2.3623-2.51030.2331450.21764032100
2.5103-2.70410.25661460.22154043100
2.7041-2.97610.25531460.21954065100
2.9761-3.40670.25041470.21134074100
3.4067-4.29170.18871460.1784403299
4.2917-48.74750.21861500.1801418898

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