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

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Basic information

Entry
Database: PDB / ID: 6lkj
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-beta-D-galactopyranose / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.004 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
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-3 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.164, 67.157, 87.600
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-BGP / 6-O-phosphono-beta-D-galactopyranose / BETA-GALACTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-galactose / 6-O-phosphono-D-galactose / 6-O-phosphono-galactose


Type: D-saccharide, beta 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
b-D-Galp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
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: 2→50 Å / Num. obs: 21110 / % possible obs: 99.3 % / Redundancy: 4.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.054 / Rrim(I) all: 0.124 / Net I/σ(I): 11.05
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.82 / Num. unique obs: 2042 / CC1/2: 0.751 / Rpim(I) all: 0.287 / Rrim(I) all: 0.565 / % 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: 2.004→28.235 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.95
RfactorNum. reflection% reflection
Rfree0.2294 1015 4.81 %
Rwork0.1951 --
obs0.1968 21110 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.9 Å2 / Biso mean: 19.1231 Å2 / Biso min: 6.12 Å2
Refinement stepCycle: final / Resolution: 2.004→28.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 16 128 2520
Biso mean--9.85 20.2 -
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022444
X-RAY DIFFRACTIONf_angle_d0.5253312
X-RAY DIFFRACTIONf_chiral_restr0.045371
X-RAY DIFFRACTIONf_plane_restr0.003425
X-RAY DIFFRACTIONf_dihedral_angle_d5.3731487
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.004-2.10930.30351350.2344280298
2.1093-2.24140.23211350.2162851100
2.2414-2.41440.24751610.21382821100
2.4144-2.65720.23351460.20662875100
2.6572-3.04130.23181410.20422904100
3.0413-3.83030.22961580.18372899100
3.8303-28.2350.19391390.1675294396

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