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- PDB-6t1z: LmrP from L. lactis, in an outward-open conformation, bound to Ho... -

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Basic information

Entry
Database: PDB / ID: 6t1z
TitleLmrP from L. lactis, in an outward-open conformation, bound to Hoechst 33342
ComponentsLmrP integral membrane protein
KeywordsTRANSPORT PROTEIN / Transmembrane multidrug transporter
Function / homology
Function and homology information


transmembrane transporter activity / 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
Chem-HT1 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE / LmrP integral membrane protein
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHutchin, A. / Debruycker, V. / Masureel, M. / Legrand, P. / Remaut, H. / Govaerts, C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2020
Title: An embedded lipid in the multidrug transporter LmrP suggests a mechanism for polyspecificity.
Authors: Debruycker, V. / Hutchin, A. / Masureel, M. / Ficici, E. / Martens, C. / Legrand, P. / Stein, R.A. / Mchaourab, H.S. / Faraldo-Gomez, J.D. / Remaut, H. / Govaerts, C.
History
DepositionOct 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 10, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: LmrP integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0277
Polymers45,2781
Non-polymers2,7496
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint7 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.76, 139.99, 115.7
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein LmrP integral membrane protein


Mass: 45277.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: lmrP / Plasmid: lmrp-pHLP5-3C
Production host: Lactococcus lactis subsp. cremoris NZ9000 (lactic acid bacteria)
References: UniProt: Q48658
#4: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 4 types, 7 molecules

#2: Chemical ChemComp-HT1 / 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE / HOECHST 33342


Mass: 452.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28N6O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-XP4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE


Mass: 591.777 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H60O8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DMPA, phospholipid*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.68 Å3/Da / Density % sol: 73.74 % / Description: Thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 80 mM SPG pH 7, 20% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97166 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97166 Å / Relative weight: 1
Reflection

Entry-ID: 6T1Z / CC1/2: 1

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Diffraction-IDNet I/σ(I)
2.9-83.8751275566.421113.36
2.9-47.721908899.519.229.1
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
2.9-2.982810.551
2.9-2.9813030.2342

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
Aimlessdata scaling
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-house structure

Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 7.664 / Cross valid method: FREE R-VALUE / SU R Blow DPI: 2.169 / SU Rfree Blow DPI: 0.382 / SU Rfree Cruickshank DPI: 0.394
RfactorNum. reflection% reflectionSelection details
Rfree0.238 654 -RANDOM
Rwork0.225 ---
obs0.225 12686 66.3 %-
Displacement parametersBiso mean: 83.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.7365 Å20 Å20 Å2
2---2.9576 Å20 Å2
3----0.7789 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2981 0 180 3 3164
LS refinement shellResolution: 2.9→3 Å
RfactorNum. reflection% reflection
Rfree0.2881 29 -
Rwork0.2548 --
obs0.2572 397 21.74 %

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