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- PDB-6xgy: Crystal structure of E. coli MlaFB ABC transport subunits in the ... -

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Basic information

Entry
Database: PDB / ID: 6xgy
TitleCrystal structure of E. coli MlaFB ABC transport subunits in the dimeric state
Components
  • ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component
  • Organic solvent ABC transporter ATP-binding protein
KeywordsLIPID TRANSPORT / ABC transporters / MlaF / MlaB / bacterial outer membrane / ATPase / regulation / STAS domain
Function / homology
Function and homology information


phospholipid transfer activity / intermembrane phospholipid transfer / phospholipid-translocating ATPase complex / phospholipid transport / ATPase-coupled transmembrane transporter activity / response to antibiotic / DNA damage response / ATP binding / membrane / cytosol
Similarity search - Function
Probable ABC transporter ATP-binding protein MlaF/Mkl / : / : / STAS domain / STAS domain / Transcription Regulator spoIIAA / STAS domain profile. / STAS domain / STAS domain superfamily / ABC transporter-like, conserved site ...Probable ABC transporter ATP-binding protein MlaF/Mkl / : / : / STAS domain / STAS domain / Transcription Regulator spoIIAA / STAS domain profile. / STAS domain / STAS domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Intermembrane phospholipid transport system binding protein MlaB / Organic solvent ABC transporter ATP-binding protein / Intermembrane phospholipid transport system binding protein MlaB
Similarity search - Component
Biological speciesEscherichia coli LAU-EC10 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChang, Y. / Bhabha, G. / Ekiert, D.C.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128777 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM112982 United States
Other privateDFS-20-16 United States
American Heart Association20POST35210202 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM088118 United States
CitationJournal: Elife / Year: 2020
Title: Structure of MlaFB uncovers novel mechanisms of ABC transporter regulation.
Authors: Kolich, L.R. / Chang, Y.T. / Coudray, N. / Giacometti, S.I. / MacRae, M.R. / Isom, G.L. / Teran, E.M. / Bhabha, G. / Ekiert, D.C.
History
DepositionJun 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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

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Assembly

Deposited unit
A: Organic solvent ABC transporter ATP-binding protein
B: ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9195
Polymers41,4432
Non-polymers4763
Water724
1
A: Organic solvent ABC transporter ATP-binding protein
B: ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component
hetero molecules

A: Organic solvent ABC transporter ATP-binding protein
B: ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,83710
Polymers82,8864
Non-polymers9526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area9350 Å2
ΔGint-99 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.710, 102.710, 89.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Organic solvent ABC transporter ATP-binding protein


Mass: 29128.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli LAU-EC10 (bacteria) / Gene: V415_03760 / Plasmid: pBEL1307 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: V8KL36
#2: Protein ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component / Lipid asymmetry maintenance protein MlaB / Phospholipid ABC transporter substrate-binding protein / ...Lipid asymmetry maintenance protein MlaB / Phospholipid ABC transporter substrate-binding protein / Phospholipid ABC transporter-binding protein / Putative anti-sigma factor antagonist / Putative phospholipid ABC transporter-binding protein MlaB


Mass: 12314.044 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mlaB, yrbB / Plasmid: pBEL1307 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: W8T4U6, UniProt: P64602*PLUS
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.3 Å3/Da / Density % sol: 62.68 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 12, 2016
RadiationMonochromator: Water-cooled flat double Si(111) Khozu monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.9→44.57 Å / Num. obs: 12466 / % possible obs: 93.09 % / Redundancy: 19.7 % / CC1/2: 0.999 / Net I/σ(I): 16.09
Reflection shellResolution: 2.9→3.004 Å / Num. unique obs: 1213 / CC1/2: 0.349

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OUK, 3F43

2ouk

3f43


Resolution: 2.9→44.57 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 586 5.05 %Random
Rwork0.1956 11026 --
obs0.1979 11612 93.13 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.18 Å2 / Biso mean: 84.1482 Å2 / Biso min: 36.55 Å2
Refinement stepCycle: final / Resolution: 2.9→44.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 29 4 2805
Biso mean--87.91 60.03 -
Num. residues----363
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.190.37731300.31472353248381
3.19-3.650.29441470.24852706285393
3.65-4.60.24661500.18222917306799
4.6-44.570.20221590.16983050320999
Refinement TLS params.Method: refined / Origin x: -35.9284 Å / Origin y: 17.9383 Å / Origin z: 3.3316 Å
111213212223313233
T0.4308 Å2-0.0806 Å20.0526 Å2-0.4277 Å2-0.0253 Å2--0.5186 Å2
L0.7546 °2-0.0016 °20.1814 °2-2.6026 °2-1.8172 °2--4.0284 °2
S0.0019 Å °0.0923 Å °0.1782 Å °0.0978 Å °-0.1389 Å °-0.1023 Å °-0.2233 Å °0.2339 Å °0.115 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 268
2X-RAY DIFFRACTION1allB-1 - 97
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allD1 - 2
5X-RAY DIFFRACTION1allE1 - 4

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