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- PDB-5uw2: Structure of E. coli MCE protein MlaD, periplasmic domain -

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Basic information

Entry
Database: PDB / ID: 5uw2
TitleStructure of E. coli MCE protein MlaD, periplasmic domain
ComponentsProbable phospholipid ABC transporter-binding protein MlaD
KeywordsTRANSPORT PROTEIN / MCE protein / bacterial lipid transport
Function / homologyMce/MlaD / Probable phospholipid ABC transporter-binding protein MlaD / MlaD protein / phospholipid transport / integral component of membrane / plasma membrane / Probable phospholipid ABC transporter-binding protein MlaD
Function and homology information
Specimen sourceEscherichia coli o157:h7 / / bacteria / image: Escherichia coli
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.85 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
1.2Sep 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 ABC transporter-binding protein MlaD
B: Probable phospholipid ABC transporter-binding protein MlaD
C: Probable phospholipid ABC transporter-binding protein MlaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3119
Polyers53,9193
Non-polymers3926
Water0
1
A: Probable phospholipid ABC transporter-binding protein MlaD
B: Probable phospholipid ABC transporter-binding protein MlaD
C: Probable phospholipid ABC transporter-binding protein MlaD
hetero molecules

A: Probable phospholipid ABC transporter-binding protein MlaD
B: Probable phospholipid ABC transporter-binding protein MlaD
C: Probable phospholipid ABC transporter-binding protein MlaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,62218
Polyers107,8376
Non-polymers78512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area (Å2)11210
ΔGint (kcal/M)-401
Surface area (Å2)33790
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)122.360, 63.820, 91.150
Angle α, β, γ (deg.)90.00, 130.01, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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Components

#1: Protein/peptide Probable phospholipid ABC transporter-binding protein MlaD


Mass: 17972.891 Da / Num. of mol.: 3 / Fragment: UNP residues 32-183
Source: (gene. exp.) Escherichia coli o157:h7 / / bacteria / image: Escherichia coli
Gene: mlaD, Z4556, ECs4072 / Production host: Escherichia coli / References: UniProt:P64605
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Formula: Zn / Zinc

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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: 2.53 / Density percent sol: 51.34
Crystal growTemp: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M zinc acetate, 0.1 M MES pH 6.0, and 15% ethanol

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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 315r / Detector: CCD / Collection date: Feb 20, 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: 2.85 Å / D resolution low: 50 Å / Number obs: 12551 / CC half: 0.47 / NetI over sigmaI: 14.9 / Redundancy: 3.7 / Percent possible obs: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UW8
Overall SU ML: 0.37 / Cross valid method: FREE R-VALUE / Sigma F: 0 / Overall phase error: 34.63
Solvent computationSolvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1 Å
Least-squares processR factor R free: 0.2648 / R factor R work: 0.2394 / R factor obs: 0.2406 / Highest resolution: 2.85 Å / Lowest resolution: 33.599 Å / Number reflection R free: 589 / Number reflection obs: 11594 / Percent reflection R free: 5.08 / Percent reflection obs: 91.09
Refine hist #LASTHighest resolution: 2.85 Å / Lowest resolution: 33.599 Å
Number of atoms included #LASTProtein: 2557 / Nucleic acid: 0 / Ligand: 6 / Solvent: 0 / Total: 2563
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032596
X-RAY DIFFRACTIONf_angle_d0.7373526
X-RAY DIFFRACTIONf_dihedral_angle_d9.530950
X-RAY DIFFRACTIONf_chiral_restr0.028426
X-RAY DIFFRACTIONf_plane_restr0.003447
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
2.85000.37830.36203.1366126235679.00
3.13660.30910.28573.5901146276792.00
3.59010.29350.24224.5214158295298.00
4.52140.23230.216633.6015159293095.00
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
13.21030.1951-0.56653.8698-2.50002.47050.07330.0872-0.35000.45040.04210.0766-0.41680.51140.00071.04820.0227-0.25740.8943-0.10311.043117.981125.742719.6262
20.5456-1.4116-0.23293.50790.58473.29310.0637-0.02660.3590-0.00730.3160-0.7627-0.54390.76080.00060.8444-0.06320.01751.0014-0.15921.241225.749825.3126-5.6183
34.2259-1.77840.94342.67670.81632.7218-0.27930.21870.2141-0.42480.0666-0.0810-0.33310.27060.00021.1164-0.13220.11270.76700.03660.78188.103125.4868-25.0812
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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