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- PDB-5uvn: Structure of E. coli MCE protein PqiB, periplasmic domain -

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Basic information

Entry
Database: PDB / ID: 5uvn
TitleStructure of E. coli MCE protein PqiB, periplasmic domain
DescriptorParaquat-inducible protein B
KeywordsTRANSPORT PROTEIN / MCE protein / bacterial lipid transport
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (3.96 Å resolution / Particle / Single particle)
AuthorsBhabha, G. / Ekiert, D.C.
CitationCell, 2017, 169, 273-285.e17

Cell, 2017, 169, 273-285.e17 Yorodumi Papers
Architectures of Lipid Transport Systems for the Bacterial Outer Membrane.
Damian C Ekiert / Gira Bhabha / Georgia L Isom / Garrett Greenan / Sergey Ovchinnikov / Ian R Henderson / Jeffery S Cox / Ronald D Vale

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 evidence / Data collectionem_image_scans / em_software / pdbx_audit_support_em_software.name / _pdbx_audit_support.funding_organization

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Assembly

Deposited unit
A: Paraquat-inducible protein B
B: Paraquat-inducible protein B
C: Paraquat-inducible protein B
D: Paraquat-inducible protein B
E: Paraquat-inducible protein B
F: Paraquat-inducible protein B


Theoretical massNumber of molelcules
Total (without water)293,1426
Polyers293,1426
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)24640
ΔGint (kcal/M)-166
Surface area (Å2)119970
MethodPISA

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Components

#1: Polypeptide(L)
Paraquat-inducible protein B


Mass: 48857.043 Da / Num. of mol.: 6
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P43671

Cellular component

Sequence detailsThe actual sample sequence is MHHHHHHENLYFQSHQGPEVTLITANAEGIEGGKTTIKSRSVDVGVVESATLADD LTHVEIKARLNSGMEKLLHKDTVFWVVKPQIGREGISGLGTLLSGVYIELQPGAK GSKMDKYDLLDSPPLAPPDAKGIRVILDSKKAGQLSPGDPVLFRGYRVGSVETST FDTQKRNISYQLFINAPYDRLVTNNVRFWKDSGIAVDLTSAGMRVEMGSLTTLLS GGVSFDVPEGLDLGQPVAPKTAFVLYDDQKSIQDSLYTDHIDYLMFFKDSVRGLQ PGAPVEFRGIRLGTVSKVPFFAPNMRQTFNDDYRIPVLIRIEPERLKMQLGENAD VVEHLGELLKRGLRGSLKTGNLVTGALYVDLDFYPNTPAITGIREFNGYQIIPTV SGGLAQIQQRLMEALDKINKLPLNPMIEQATSTLSESQRTMKNLQTTLDSMNKIL ASQSMQQLPTDMQSTLRELNRSMQGFQPGSAAYNKMVADMQRLDQVLRELQPVLK TLNEKSNALVFEAKDKKDPEPKRAKQ

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: homo hexamer of PqiB / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.347 deg. / Units: MEGADALTONS
Source (natural)Organism: Escherichia coli / Strain: K12
Source (recombinant)Organism: Escherichia coli
Buffer solutionDetails: 20 mM Tris pH 8.0 and 150 mM NaCl / pH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil 1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 80 e/Å2 / Details: 80 e/A2 is total dose for 50 frames / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDFitting ID
4Gctf0.5CTF CORRECTION1
7Coot0.8.1MODEL FITTING1
9RELION1.4INITIAL EULER ASSIGNMENT1
10RELION1.4FINAL EULER ASSIGNMENT1
11RELION1.4CLASSIFICATION1
12RELION1.4RECONSTRUCTION1
13PHENIX1.9MODEL REFINEMENT1
CTF correctionType: NONE
SymmetryPoint symmetry: C6
3D reconstructionResolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 36591 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL
Least-squares processHighest resolution: 3.96 Å

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