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- PDB-4mt4: Crystal structure of the Campylobacter jejuni CmeC outer membrane... -

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Basic information

Entry
Database: PDB / ID: 4mt4
TitleCrystal structure of the Campylobacter jejuni CmeC outer membrane channel
ComponentsCmeC
KeywordsTRANSPORT PROTEIN / beta barrel
Function / homology
Function and homology information


efflux transmembrane transporter activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / RND efflux system, outer membrane lipoprotein, NodT / Outer membrane efflux protein / Outer membrane efflux protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(2S)-1-(pentanoyloxy)propan-2-yl hexanoate / CmeC
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.373 Å
AuthorsSu, C.-C. / Yu, E.W.
CitationJournal: Protein Sci. / Year: 2014
Title: Crystal structure of the Campylobacter jejuni CmeC outer membrane channel.
Authors: Su, C.C. / Radhakrishnan, A. / Kumar, N. / Long, F. / Bolla, J.R. / Lei, H.T. / Delmar, J.A. / Do, S.V. / Chou, T.H. / Rajashankar, K.R. / Zhang, Q. / Yu, E.W.
History
DepositionSep 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CmeC
B: CmeC
C: CmeC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,42026
Polymers162,9373
Non-polymers6,48323
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29820 Å2
ΔGint-115 kcal/mol
Surface area62730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.827, 146.324, 418.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CmeC


Mass: 54312.305 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: cmeC / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RTE3
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-3PK / (2S)-1-(pentanoyloxy)propan-2-yl hexanoate


Mass: 258.354 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H26O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 4.32 Å3/Da / Density % sol: 71.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: 30 PEG400, 0.2M NK4SO4, 0.1M NaAC (5.0), VAPOR DIFFUSION, temperature 298K

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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 315 / Detector: CCD / Date: Jun 26, 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: 2.37→100 Å / Num. all: 204082 / Num. obs: 204082 / % possible obs: 93.7 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 1.8 % / Biso Wilson estimate: 45.09 Å2 / Rmerge(I) obs: 0.109 / Χ2: 1.969 / Net I/σ(I): 5.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.37-2.461.70.488209901.027186.6
2.46-2.581.70.45225311.058193.4
2.58-2.711.70.336216101.211189.3
2.71-2.881.80.247237981.414198.3
2.88-3.111.80.192237431.716198.3
3.11-3.421.80.145229132.139194.5
3.42-3.911.80.103228282.773194.3
3.91-4.931.80.086230043.306195.4
4.93-1001.80.072226652.772193.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIXdev_1439refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.373→100 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.7905 / SU ML: 0.31 / σ(F): 18.54 / Phase error: 28.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 5618 5.01 %RANDOM
Rwork0.2097 ---
obs0.2114 112225 98.2 %-
all-112225 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.11 Å2 / Biso mean: 55.68 Å2 / Biso min: 20.49 Å2
Refinement stepCycle: LAST / Resolution: 2.373→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11304 0 434 559 12297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211933
X-RAY DIFFRACTIONf_angle_d0.49215978
X-RAY DIFFRACTIONf_chiral_restr0.021691
X-RAY DIFFRACTIONf_plane_restr0.0022031
X-RAY DIFFRACTIONf_dihedral_angle_d14.3434594
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3725-2.39950.35541400.30223150329085
2.3995-2.42770.32221610.27853515367699
2.4277-2.45730.32971700.2773584375499
2.4573-2.48840.31382290.26353476370599
2.4884-2.52120.30481910.2693549374099
2.5212-2.55570.32831870.25633577376499
2.5557-2.59220.35392010.25293452365399
2.5922-2.63090.30772160.24483534375098
2.6309-2.6720.27321910.23833462365397
2.672-2.71580.30561970.22843502369997
2.7158-2.76270.31022120.237435523764100
2.7627-2.81290.31231890.223560374999
2.8129-2.8670.26341870.21823608379599
2.867-2.92550.29021640.21873511367599
2.9255-2.98920.27221910.221636293820100
2.9892-3.05870.2541860.210336053791100
3.0587-3.13520.26841720.219835523724100
3.1352-3.220.24171850.21023604378999
3.22-3.31470.2481920.22623607379999
3.3147-3.42170.25531760.22563496367298
3.4217-3.5440.24871690.223537370697
3.544-3.68590.24451860.20433591377799
3.6859-3.85370.23131970.18983599379699
3.8537-4.05690.221980.18183574377299
4.0569-4.3110.21791970.17733607380498
4.311-4.64390.21312070.1833546375398
4.6439-5.11120.17531650.17333596376197
5.1112-5.85080.20851900.20233597378798
5.8508-7.37110.22681660.21543703386999
7.3711-104.81860.21892060.2143732393896

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