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- PDB-5t0o: Crystal Structure of a membrane protein -

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Basic information

Entry
Database: PDB / ID: 5t0o
TitleCrystal Structure of a membrane protein
ComponentsCmeB
KeywordsMEMBRANE PROTEIN / transmembrane protein
Function / homology
Function and homology information


xenobiotic transport / efflux transmembrane transporter activity / 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
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.15 Å
AuthorsSu, C.-C. / Yu, E.W.
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 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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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


Theoretical massNumber of molelcules
Total (without water)342,1813
Polymers342,1813
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20790 Å2
ΔGint-127 kcal/mol
Surface area114380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)300.71, 147.538, 120.027
Angle α, β, γ (deg.)90, 99.87, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CmeB


Mass: 114060.273 Da / Num. of mol.: 3 / Mutation: C1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: cmeB / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RTE4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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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: 3.83 Å3/Da / Density % sol: 67.91 % / Mosaicity: 0.198 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5 / Details: 4% PEG8000, 0.1M MgSo4, 0.1M MES (6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2013
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.15→100 Å / Num. obs: 158913 / % possible obs: 90.7 % / Redundancy: 1.6 % / Biso Wilson estimate: 57.23 Å2 / Rmerge(I) obs: 0.103 / Χ2: 1.232 / Net I/av σ(I): 6.574 / Net I/σ(I): 6.7 / Num. measured all: 251867
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.6 % / Rejects: _

Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
3.15-3.260.483159051.08490.7
3.26-3.390.356159541.05590.9
3.39-3.550.258158671.05390.7
3.55-3.730.193159481.07591
3.73-3.970.131160251.08391.1
3.97-4.280.091159311.13591
4.28-4.710.074158691.35991
4.71-5.390.087159741.73490.8
5.39-6.790.095157411.76589.9
6.79-1000.024156991.00889.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 3.15→84.93 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2678 4018 -
Rwork0.2109 --
obs0.2139 79625 89.13 %
Refinement stepCycle: LAST / Resolution: 3.15→84.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23876 0 0 25 23901

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