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- PDB-4dk0: Crystal structure of MacA from Actinobacillus actinomycetemcomitans -

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Basic information

Entry
Database: PDB / ID: 4dk0
TitleCrystal structure of MacA from Actinobacillus actinomycetemcomitans
ComponentsPutative MacA
KeywordsMEMBRANE PROTEIN / alpha-hairpin / lipoyl / beta-barrel / PERIPLASMIC PROTEIN
Function / homology
Function and homology information


macrolide transmembrane transporter complex / xenobiotic detoxification by transmembrane export across the plasma membrane / extrinsic component of membrane / transmembrane transporter activity / identical protein binding
Similarity search - Function
Macrolide export protein MacA / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Efflux pump adaptor protein, beta barrel domain / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Elongation Factor Tu (Ef-tu); domain 3 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...Macrolide export protein MacA / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Efflux pump adaptor protein, beta barrel domain / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Elongation Factor Tu (Ef-tu); domain 3 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesAggregatibacter actinomycetemcomitans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.5 Å
AuthorsXu, Y. / Piao, S. / Ha, N.C.
CitationJournal: J Biol Chem / Year: 2012
Title: Assembly and channel opening of outer membrane protein in tripartite drug efflux pumps of Gram-negative bacteria.
Authors: Yongbin Xu / Arne Moeller / So-Young Jun / Minho Le / Bo-Young Yoon / Jin-Sik Kim / Kangseok Lee / Nam-Chul Ha /
Abstract: Gram-negative bacteria are capable of expelling diverse xenobiotic substances from within the cell by use of three-component efflux pumps in which the energy-activated inner membrane transporter is ...Gram-negative bacteria are capable of expelling diverse xenobiotic substances from within the cell by use of three-component efflux pumps in which the energy-activated inner membrane transporter is connected to the outer membrane channel protein via the membrane fusion protein. In this work, we describe the crystal structure of the membrane fusion protein MexA from the Pseudomonas aeruginosa MexAB-OprM pump in the hexameric ring arrangement. Electron microscopy study on the chimeric complex of MexA and the outer membrane protein OprM reveals that MexA makes a tip-to-tip interaction with OprM, which suggests a docking model for MexA and OprM. This docking model agrees well with genetic results and depicts detailed interactions. Opening of the OprM channel is accompanied by the simultaneous exposure of a protein structure resembling a six-bladed cogwheel, which intermeshes with the complementary cogwheel structure in the MexA hexamer. Taken together, we suggest an assembly and channel opening model for the MexAB-OprM pump. This study provides a better understanding of multidrug resistance in Gram-negative bacteria.
History
DepositionFeb 3, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative MacA


Theoretical massNumber of molelcules
Total (without water)39,8671
Polymers39,8671
Non-polymers00
Water0
1
A: Putative MacA
x 12


Theoretical massNumber of molelcules
Total (without water)478,40012
Polymers478,40012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_775-x+2,-y+2,z1
crystal symmetry operation5_565y,-x+y+1,z1
crystal symmetry operation6_655x-y+1,x,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
crystal symmetry operation9_765-x+2,-x+y+1,-z1
crystal symmetry operation10_775-y+2,-x+2,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
crystal symmetry operation12_565x,x-y+1,-z1
Buried area50480 Å2
ΔGint-186 kcal/mol
Surface area186660 Å2
MethodPISA
2
A: Putative MacA
x 6


Theoretical massNumber of molelcules
Total (without water)239,2006
Polymers239,2006
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_775-x+2,-y+2,z1
crystal symmetry operation5_565y,-x+y+1,z1
crystal symmetry operation6_655x-y+1,x,z1
Buried area22300 Å2
ΔGint-73 kcal/mol
Surface area96260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.188, 109.188, 255.442
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Putative MacA


Mass: 39866.645 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 30-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aggregatibacter actinomycetemcomitans (bacteria)
Gene: macA / Production host: Escherichia coli (E. coli) / References: UniProt: Q2EHL9
Sequence detailsTHESE RESIDUES DERIVE FROM A VARIANT OF THE STRAIN OF THE BACTERIA

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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: 5.51 Å3/Da / Density % sol: 77.69 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 8.5
Details: 0.01M Nickel chloride, 0.1M Tris-HCl, 1M Lithium Sulfate, pH 8.5, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.0000, 0.9794, 0.9796, 1.1271
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 15, 2008
RadiationMonochromator: Double mirror / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97941
30.97961
41.12711
ReflectionResolution: 3→50 Å / Num. all: 18344 / Num. obs: 17810 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3→3.11 Å / % possible all: 87.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.5→9.991 Å / SU ML: 1.08 / σ(F): 0.17 / Phase error: 40.2 / Stereochemistry target values: MLHL
Details: THE AUTHOR DID NOT USE THE DATA IN 3.5-3.0A SINCE THE R-FACTOR WAS NOT REASONABLE AND THE MAP QUALITY LOOKED LIKE 3.5A RESOLUTION MAP.
RfactorNum. reflection% reflectionSelection details
Rfree0.3899 1124 10 %random
Rwork0.3384 ---
all0.3435 11237 --
obs0.3435 11237 97.93 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 111.379 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.0066 Å2-0 Å2-0 Å2
2--10.0066 Å20 Å2
3----20.0131 Å2
Refinement stepCycle: LAST / Resolution: 3.5→9.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 0 0 2486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152506
X-RAY DIFFRACTIONf_angle_d2.0953400
X-RAY DIFFRACTIONf_dihedral_angle_d23.443933
X-RAY DIFFRACTIONf_chiral_restr0.142428
X-RAY DIFFRACTIONf_plane_restr0.007434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.65180.37271390.3661260X-RAY DIFFRACTION99
3.6518-3.8340.41761340.36951206X-RAY DIFFRACTION98
3.834-4.0590.44551380.35661238X-RAY DIFFRACTION97
4.059-4.34830.37331380.32381235X-RAY DIFFRACTION97
4.3483-4.74290.41961390.31281252X-RAY DIFFRACTION97
4.7429-5.33570.38591410.33151272X-RAY DIFFRACTION99
5.3357-6.41230.40741450.36881302X-RAY DIFFRACTION99
6.4123-9.99080.35021500.32251348X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 80.678 Å / Origin y: 104.0272 Å / Origin z: 76.7551 Å
111213212223313233
T0.4275 Å2-0.2237 Å2-0.0246 Å2-0.5567 Å2-0.0912 Å2--0.3243 Å2
L0.4893 °20.3294 °20.2566 °2-0.5207 °20.3151 °2--1.8577 °2
S0.3783 Å °-0.215 Å °0.0439 Å °0.122 Å °-0.316 Å °-0.1284 Å °-0.2703 Å °0.3041 Å °-0.1205 Å °
Refinement TLS groupSelection details: all

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