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

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Basic information

Entry
Database: PDB / ID: 6lkl
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
MALONIC ACID / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.213 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: ABC transporter, solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7174
Polymers67,5092
Non-polymers2082
Water3,513195
1
A: ABC transporter, solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8582
Polymers33,7541
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter, solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8582
Polymers33,7541
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.375, 85.932, 71.515
Angle α, β, γ (deg.)90.000, 96.740, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 29 - 322 / Label seq-ID: 1 - 294

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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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.: 2
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: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 60% Tascimate 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 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: 2.21→50 Å / Num. obs: 41995 / % possible obs: 98 % / Redundancy: 3.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.063 / Rrim(I) all: 0.119 / Net I/σ(I): 9.1
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.411 / Num. unique obs: 4135 / CC1/2: 0.85 / Rpim(I) all: 0.259 / Rrim(I) all: 0.488 / % possible all: 97.2

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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: 2.213→45.358 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2001 2114 5.03 %
Rwork0.1705 39881 -
obs0.172 41995 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.04 Å2 / Biso mean: 35.9202 Å2 / Biso min: 12.63 Å2
Refinement stepCycle: final / Resolution: 2.213→45.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4752 0 18 195 4965
Biso mean--31.6 34.34 -
Num. residues----588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034868
X-RAY DIFFRACTIONf_angle_d0.736590
X-RAY DIFFRACTIONf_chiral_restr0.048732
X-RAY DIFFRACTIONf_plane_restr0.004854
X-RAY DIFFRACTIONf_dihedral_angle_d15.1192976
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3621X-RAY DIFFRACTION7.855TORSIONAL
12B3621X-RAY DIFFRACTION7.855TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.213-2.26420.23521330.2148261196
2.2642-2.32080.24671520.2023264898
2.3208-2.38360.22011370.195262597
2.3836-2.45370.2451380.1919261697
2.4537-2.53290.20831320.1823263497
2.5329-2.62340.24071250.1828263498
2.6234-2.72850.24151390.1905269098
2.7285-2.85260.20911490.1783263098
2.8526-3.0030.22741410.1853263598
3.003-3.19110.19911380.1731268598
3.1911-3.43740.19491480.1677266899
3.4374-3.78320.18391440.1528268799
3.7832-4.33020.15871440.1394267598
4.3302-5.45420.17951470.1442271199
5.4542-45.3580.19491470.1881273298

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