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- PDB-5lq3: Structures and transport dynamics of the Campylobacter jejuni mul... -

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Basic information

Entry
Database: PDB / ID: 5lq3
TitleStructures and transport dynamics of the Campylobacter jejuni multidrug efflux pump CmeB
ComponentsCmeB
KeywordsTRANSPORT PROTEIN / transmembrane protein
Function / homology
Function and homology information


xenobiotic transport / efflux transmembrane transporter activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein ...Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Efflux pump membrane transporter / Efflux pump membrane transporter
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsSu, C.C.
CitationJournal: Nat Commun / Year: 2017
Title: Structures and transport dynamics of a Campylobacter jejuni multidrug efflux pump.
Authors: Su, C.C. / Yin, L. / Kumar, N. / Dai, L. / Radhakrishnan, A. / Bolla, J.R. / Lei, H.T. / Chou, T.H. / Delmar, J.A. / Rajashankar, K.R. / Zhang, Q. / Shin, Y.K. / Yu, E.W.
History
DepositionAug 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CmeB
B: CmeB
C: CmeB
D: CmeB
E: CmeB
F: CmeB


Theoretical massNumber of molelcules
Total (without water)681,0466
Polymers681,0466
Non-polymers00
Water00
1
A: CmeB
B: CmeB
C: CmeB


Theoretical massNumber of molelcules
Total (without water)340,5233
Polymers340,5233
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19510 Å2
ΔGint-81 kcal/mol
Surface area116450 Å2
MethodPISA
2
D: CmeB
E: CmeB
F: CmeB


Theoretical massNumber of molelcules
Total (without water)340,5233
Polymers340,5233
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19350 Å2
ΔGint-79 kcal/mol
Surface area115270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.868, 127.987, 169.606
Angle α, β, γ (deg.)99.790, 99.450, 84.950
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
CmeB


Mass: 113507.672 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: cmeB / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RTE4, UniProt: Q0PBE4*PLUS

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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: 3.74 Å3/Da / Density % sol: 67.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 4% PEG8000 20mM NaMES 0.1M MgSO4 / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.55→100 Å / Num. obs: 109703 / % possible obs: 91.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 95.24 Å2 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.114 / Rrim(I) all: 0.171 / Χ2: 1.07 / Net I/σ(I): 6.2 / Num. measured all: 408878
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.55-3.683.7113310.490.7691.0394.1
3.68-3.823.7112740.6880.5351.05294.10.894
3.82-43.7111190.8140.41.0892.70.6660.778
4-4.213.7109950.9090.2571.08591.20.4310.502
4.21-4.473.7104560.9520.1651.10887.20.2750.321
4.47-4.823.7105660.9770.1121.06287.90.1860.218
4.82-5.33.8114110.980.1021.06394.60.1720.2
5.3-6.073.8110470.9780.1081.085920.1810.211
6.07-7.653.7104990.9870.0691.05287.40.1150.134
7.65-1003.7110050.9960.0351.08391.70.0570.067

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V50

2v50


Resolution: 3.55→90.27 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2677 5483 5.01 %
Rwork0.2263 104045 -
obs0.2284 109528 89.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 190.57 Å2 / Biso mean: 100.92 Å2 / Biso min: 51.67 Å2
Refinement stepCycle: final / Resolution: 3.55→90.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47878 0 0 0 47878
Num. residues----6202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00248814
X-RAY DIFFRACTIONf_angle_d0.52266242
X-RAY DIFFRACTIONf_chiral_restr0.0397804
X-RAY DIFFRACTIONf_plane_restr0.0048418
X-RAY DIFFRACTIONf_dihedral_angle_d13.56429244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5196-3.55960.41451100.34031722183245
3.5596-3.60150.39072020.33273646384894
3.6015-3.64540.36551870.33383638382594
3.6454-3.69150.34641750.31523645382094
3.6915-3.74010.32091720.31483686385894
3.7401-3.79130.33312070.29463594380194
3.7913-3.84550.31111750.2793601377693
3.8455-3.90290.32432020.27013625382793
3.9029-3.96390.2952020.25433526372892
3.9639-4.02890.33991720.25883585375792
4.0289-4.09830.28451840.24343525370991
4.0983-4.17290.33152070.24393538374591
4.1729-4.25310.28891930.23433439363290
4.2531-4.33990.2961830.22443415359888
4.3399-4.43430.26821760.21453300347686
4.4343-4.53750.24371650.19972997316278
4.5375-4.65090.26681760.20163400357688
4.6509-4.77670.24841870.19673709389695
4.7767-4.91720.22091920.20193653384595
4.9172-5.07590.22842000.19893661386195
5.0759-5.25730.25031830.20353702388594
5.2573-5.46780.2711780.21923583376193
5.4678-5.71660.27771700.22073586375692
5.7166-6.01790.26942010.23453519372091
6.0179-6.39490.30081690.24713387355688
6.3949-6.88850.28141560.21873011316778
6.8885-7.58140.25191930.20173761395496
7.5814-8.67760.19651970.16083683388095
8.6776-10.92990.16741920.14813548374092
10.9299-90.30010.27121770.26273360353787

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