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- PDB-5uwa: Structure of E. coli phospholipid binding protein MlaC -

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Basic information

Entry
Database: PDB / ID: 5uwa
TitleStructure of E. coli phospholipid binding protein MlaC
ComponentsProbable phospholipid-binding protein MlaC
KeywordsTRANSPORT PROTEIN / phospholipid-binding protein / bacterial lipid transport
Function / homologyToluene tolerance Ttg2/phospholipid-binding protein MlaC / MlaC protein / phospholipid transport / outer membrane-bounded periplasmic space / Probable phospholipid-binding protein MlaC
Function and homology information
Specimen sourceEscherichia coli / / bacteria /
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.501 Å resolution
AuthorsBhabha, G. / Ekiert, D.C.
CitationJournal: Cell / Year: 2017
Title: Architectures of Lipid Transport Systems for the Bacterial Outer Membrane.
Authors: Damian C Ekiert / Gira Bhabha / Georgia L Isom / Garrett Greenan / Sergey Ovchinnikov / Ian R Henderson / Jeffery S Cox / Ronald D Vale
Abstract: How phospholipids are trafficked between the bacterial inner and outer membranes through the hydrophilic space of the periplasm is not known. We report that members of the mammalian cell entry (MCE) ...How phospholipids are trafficked between the bacterial inner and outer membranes through the hydrophilic space of the periplasm is not known. We report that members of the mammalian cell entry (MCE) protein family form hexameric assemblies with a central channel capable of mediating lipid transport. The E. coli MCE protein, MlaD, forms a ring associated with an ABC transporter complex in the inner membrane. A soluble lipid-binding protein, MlaC, ferries lipids between MlaD and an outer membrane protein complex. In contrast, EM structures of two other E. coli MCE proteins show that YebT forms an elongated tube consisting of seven stacked MCE rings, and PqiB adopts a syringe-like architecture. Both YebT and PqiB create channels of sufficient length to span the periplasmic space. This work reveals diverse architectures of highly conserved protein-based channels implicated in the transport of lipids between the membranes of bacteria and some eukaryotic organelles.
Copyright: 2017 Elsevier Inc. All rights reserved.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 20, 2017 / Release: Apr 12, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 12, 2017Structure modelrepositoryInitial release
1.1Apr 19, 2017Structure modelDatabase references
1.2Aug 9, 2017Structure modelDatabase referencespdbx_related_exp_data_set
1.3Sep 27, 2017Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable phospholipid-binding protein MlaC
B: Probable phospholipid-binding protein MlaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2494
Polyers47,0252
Non-polymers1,2242
Water5,206289
1
A: Probable phospholipid-binding protein MlaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1252
Polyers23,5131
Non-polymers6121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable phospholipid-binding protein MlaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1252
Polyers23,5131
Non-polymers6121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)33.630, 115.890, 133.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide Probable phospholipid-binding protein MlaC


Mass: 23512.613 Da / Num. of mol.: 2
Source: (gene. exp.) Escherichia coli (strain k12) / / bacteria /
Strain: K12 / Gene: mlaC, yrbC, b3192, JW3159 / Production host: Escherichia coli / References: UniProt:P0ADV7
#2: Chemical ChemComp-8ND / (2S)-3-(2-aminoethoxy)propane-1,2-diyl dihexadecanoate


Mass: 611.979 Da / Num. of mol.: 2 / Formula: C37H73NO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Formula: H2O / Water

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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: 2.76 / Density percent sol: 55.44
Crystal growTemp: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M citric acid pH 3.5 and 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: ALS BEAMLINE 8.3.1 / Synchrotron site: ALS / Beamline: 8.3.1 / Wavelength: 1.116
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Collection date: May 21, 2015
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionD resolution high: 1.5 Å / D resolution low: 50 Å / Number obs: 83295 / CC half: 0.57 / NetI over sigmaI: 22.2 / Redundancy: 7.2 / Percent possible obs: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: based on homology model with 2QGU as a template
Overall SU ML: 0.16 / Cross valid method: FREE R-VALUE / Sigma F: 0 / Overall phase error: 17.02
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.2 Å
Least-squares processR factor R free: 0.1675 / R factor R work: 0.138 / R factor obs: 0.1387 / Highest resolution: 1.501 Å / Lowest resolution: 43.718 Å / Number reflection R free: 1894 / Number reflection obs: 79050 / Percent reflection R free: 2.4 / Percent reflection obs: 93.56
Refine hist #LASTHighest resolution: 1.501 Å / Lowest resolution: 43.718 Å
Number of atoms included #LASTProtein: 2978 / Nucleic acid: 0 / Ligand: 80 / Solvent: 289 / Total: 3347
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093310
X-RAY DIFFRACTIONf_angle_d1.2024497
X-RAY DIFFRACTIONf_dihedral_angle_d14.1561316
X-RAY DIFFRACTIONf_chiral_restr0.046478
X-RAY DIFFRACTIONf_plane_restr0.006590
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
1.50120.32450.25931.5387119466080.00
1.53870.26420.20641.5803114482584.00
1.58030.23920.18101.6268123505087.00
1.62680.23140.16141.6793130522289.00
1.67930.18990.13601.7394130532092.00
1.73940.19660.12391.8090131542793.00
1.80900.17400.11401.8913134557195.00
1.89130.17060.10761.9910140566397.00
1.99100.16120.10682.1158141574698.00
2.11580.15690.10872.2791142577398.00
2.27910.15330.12122.5085144581899.00
2.50850.16180.13852.8714146592099.00
2.87140.13810.14293.6174147594899.00
3.61740.17030.150443.7366153621399.00

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