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- PDB-6s7v: Lipoteichoic acids flippase LtaA -

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Basic information

Entry
Database: PDB / ID: 6s7v
TitleLipoteichoic acids flippase LtaA
ComponentsMFS transporter
KeywordsTRANSPORT PROTEIN / Lipoteichoic acids / Flippase
Function / homology
Function and homology information


lipoteichoic acid biosynthetic process / antiporter activity / lipid transport / transmembrane transporter activity / : / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
MFS transporter / Proton-coupled antiporter flippase LtaA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.301 Å
AuthorsZhang, B. / Perez, C.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationPP00P3_170607 Switzerland
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2020
Title: Structure of a proton-dependent lipid transporter involved in lipoteichoic acids biosynthesis.
Authors: Zhang, B. / Liu, X. / Lambert, E. / Mas, G. / Hiller, S. / Veening, J.W. / Perez, C.
History
DepositionJul 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MFS transporter


Theoretical massNumber of molelcules
Total (without water)42,5051
Polymers42,5051
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.390, 162.470, 191.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MFS transporter


Mass: 42504.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: BTN44_07740, FA040_03480, RK64_05390 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A2I7Y6V2, UniProt: Q2FZP8*PLUS

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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: 4.38 Å3/Da / Density % sol: 71.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 9.5 / Details: Glycine: MgAcetate:PEG300

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Data collection

DiffractionMean temperature: 289 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.3→19.996 Å / Num. obs: 10414 / % possible obs: 83.9 % / Redundancy: 14 % / Biso Wilson estimate: 93.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rrim(I) all: 0.135 / Χ2: 1.466 / Net I/σ(I): 12.76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.32-3.43141.4993.417470.9441.53734.6
3.43-3.5521.671.7512.8210260.9181.79351.2
3.55-3.6921.5941.3663.5413780.9781.39970.1
3.69-3.8421.7681.2354.0515500.9651.26483.5
3.84-4.0121.6420.915.5617440.9850.93195.7
4.01-4.2121.4740.6856.5317320.9930.70299.9
4.21-4.4321.0060.3610.1216230.9970.369100
4.43-4.719.0610.21612.3215700.9980.22199.4
4.7-5.0321.090.2214.0714500.9980.225100
5.03-5.4322.6110.17616.113520.9990.18100
5.43-5.9522.3260.21616.0512490.9980.221100
5.95-6.6522.0630.19117.9611320.9980.196100
6.65-7.6820.9660.12924.29980.9980.132100
7.68-9.418.5330.07632.788440.9990.07899.3
9.4-13.320.880.06149.096420.9990.063100
13.3-19.99621.2660.0556.163500.9990.05297.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 3.301→19.996 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2894 502 4.82 %
Rwork0.2705 9912 -
obs0.2714 10414 83.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 269.85 Å2 / Biso mean: 104.9877 Å2 / Biso min: 13.63 Å2
Refinement stepCycle: final / Resolution: 3.301→19.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3001 0 0 0 3001
Num. residues----378
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.301-3.63110.3196790.2781131246
3.6311-4.15240.25641300.2594258689
4.1524-5.21620.28191590.25852945100
5.2162-19.9960.30641340.28343069100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.2950.24310.3711.1872-0.26620.55170.12191.14730.8743-0.35560.0379-0.1045-0.1856-0.01290.0810.1939-0.02830.38530.37310.50420.3159-4.296126.534834.5812
25.67662.9302-0.07536.74173.031.8983-0.67-0.18740.1525-1.90760.73821.2665-0.53041.87960.04492.9410.8544-0.03153.47661.01411.63718.5297133.979811.4847
31.7208-1.4460.58753.6794-0.66825.25630.02951.7322-1.4329-0.6188-0.01530.32021.5861-0.47510.23631.09420.05770.04191.3973-0.63611.1756-5.0988104.431226.5715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 194 )A16 - 194
2X-RAY DIFFRACTION2chain 'A' and (resid 195 through 210 )A195 - 210
3X-RAY DIFFRACTION3chain 'A' and (resid 211 through 393 )A211 - 393

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