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- PDB-3fpp: Crystal structure of E.coli MacA -

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Basic information

Entry
Database: PDB / ID: 3fpp
TitleCrystal structure of E.coli MacA
ComponentsMacrolide-specific efflux protein macA
KeywordsMEMBRANE PROTEIN / Hexameric assembly / membrane fusion protein / drug efflux pump / periplasmic protein / Antibiotic resistance / Cell inner membrane / Cell membrane / Membrane / Transport
Function / homology
Function and homology information


MacAB-TolC complex / efflux pump complex / xenobiotic detoxification by transmembrane export across the plasma membrane / extrinsic component of membrane / efflux transmembrane transporter activity / response to antibiotic / membrane / identical protein binding / plasma membrane
Similarity search - Function
Helix Hairpins - #1990 / Macrolide export protein MacA / 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 / Helix Hairpins / Elongation Factor Tu (Ef-tu); domain 3 / Helix non-globular ...Helix Hairpins - #1990 / Macrolide export protein MacA / 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 / Helix Hairpins / Elongation Factor Tu (Ef-tu); domain 3 / Helix non-globular / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Macrolide export protein MacA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsYum, S. / Xu, Y. / Piao, S. / Ha, N.-C.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of the periplasmic component of a tripartite macrolide-specific efflux pump
Authors: Yum, S. / Xu, Y. / Piao, S. / Sim, S.-H. / Kim, H.-M. / Jo, W.-S. / Kim, K.-J. / Kweon, H.-S. / Jeong, M.-H. / Jeon, H. / Lee, K. / Ha, N.-C.
History
DepositionJan 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrolide-specific efflux protein macA
B: Macrolide-specific efflux protein macA


Theoretical massNumber of molelcules
Total (without water)74,3742
Polymers74,3742
Non-polymers00
Water0
1
A: Macrolide-specific efflux protein macA
B: Macrolide-specific efflux protein macA

A: Macrolide-specific efflux protein macA
B: Macrolide-specific efflux protein macA

A: Macrolide-specific efflux protein macA
B: Macrolide-specific efflux protein macA


Theoretical massNumber of molelcules
Total (without water)223,1236
Polymers223,1236
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area23130 Å2
ΔGint-95 kcal/mol
Surface area78300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.517, 128.517, 110.311
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Macrolide-specific efflux protein macA


Mass: 37187.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: macA / Plasmid: pPROEXHTA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P75830
Sequence detailsTHESE RESIDUES DERIVE FROM A VARIANT OF E.COLI K12 STRAIN.

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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: 3.54 Å3/Da / Density % sol: 65.21 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1M potassium sodium tartrate tetrahydrate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 5, 2008 / Details: double mirrors
RadiationMonochromator: double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. all: 21498 / Num. obs: 19873 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 0.5 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 7
Reflection shellResolution: 2.99→3.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2 / Num. unique all: 1778 / Rsym value: 0.338 / % possible all: 84.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The unrefined structure of Actinobacillus actinomycetemcomitans MacA

Resolution: 2.99→49.69 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 90818.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.349 1950 9.8 %RANDOM
Rwork0.283 ---
all0.293 19873 --
obs0.283 18206 92 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.0961 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å20 Å20 Å2
2--2.36 Å20 Å2
3----4.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.67 Å
Refinement stepCycle: LAST / Resolution: 2.99→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4097 0 0 0 4097
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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