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

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Basic information

Entry
Database: PDB / ID: 6lkk
TitleTwo-component system protein mediate signal transduction
ComponentsABC transporter, solute-binding protein
KeywordsSIGNALING PROTEIN / two-component system / G6P sensor / signal transduction
Function / homology
Function and homology information


thiamine binding / thiamine transport / thiamine pyrophosphate binding / outer membrane-bounded periplasmic space
Similarity search - Function
Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-alpha-D-glucopyranose / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.502 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

Downloads & links

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Assembly

Deposited unit
A: ABC transporter, solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0142
Polymers33,7541
Non-polymers2601
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-4 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.150, 67.444, 87.393
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 33754.316 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: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M Tris pH 7.5-7.9, 21% PEG 3350 / PH range: 7.5-7.9

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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 6M / Detector: PIXEL / Date: Sep 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 47810 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.021 / Rrim(I) all: 0.074 / Net I/σ(I): 15.36
Reflection shellResolution: 1.5→1.56 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.42 / Num. unique obs: 3920 / CC1/2: 0.986 / Rpim(I) all: 0.135 / Rrim(I) all: 0.497 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 1.502→37.307 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.01
RfactorNum. reflection% reflection
Rfree0.1958 2407 5.04 %
Rwork0.1746 --
obs0.1757 47805 95.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.91 Å2 / Biso mean: 28.3628 Å2 / Biso min: 13.99 Å2
Refinement stepCycle: final / Resolution: 1.502→37.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 27 315 2718
Biso mean--21.65 33.36 -
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032444
X-RAY DIFFRACTIONf_angle_d0.6123312
X-RAY DIFFRACTIONf_chiral_restr0.047371
X-RAY DIFFRACTIONf_plane_restr0.004425
X-RAY DIFFRACTIONf_dihedral_angle_d13.7841487
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5023-1.53290.31121070.2693217878
1.5329-1.56630.27271120.257226483
1.5663-1.60270.28171180.249244589
1.6027-1.64280.2621510.2384260895
1.6428-1.68720.24251470.2248267997
1.6872-1.73680.23621530.2083267898
1.7368-1.79290.23531480.1996270298
1.7929-1.8570.22551180.194273698
1.857-1.93130.23191410.2221272198
1.9313-2.01920.19881460.1808272599
2.0192-2.12570.19411700.1707271299
2.1257-2.25880.22371430.1882276999
2.2588-2.43320.18721540.1671276299
2.4332-2.6780.16981300.1612279499
2.678-3.06530.17061560.16772812100
3.0653-3.86140.19351520.16022822100
3.8614-37.3070.17071610.15342991100

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