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- PDB-3mku: Structure of a Cation-bound Multidrug and Toxin Compound Extrusio... -

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Basic information

Entry
Database: PDB / ID: 3mku
TitleStructure of a Cation-bound Multidrug and Toxin Compound Extrusion (MATE) transporter
ComponentsMulti antimicrobial extrusion protein (Na(+)/drug antiporter) MATE-like MDR efflux pump
KeywordsTRANSPORT PROTEIN / MATE / multidrug transporter / cation-bound
Function / homologyRUBIDIUM ION / :
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsHe, X. / Szewczyk, P. / Karyakin, A. / Evin, M. / Hong, W.-X. / Zhang, Q. / Chang, G.
CitationJournal: Nature / Year: 2010
Title: Structure of a cation-bound multidrug and toxic compound extrusion transporter.
Authors: He, X. / Szewczyk, P. / Karyakin, A. / Evin, M. / Hong, W.X. / Zhang, Q. / Chang, G.
History
DepositionApr 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multi antimicrobial extrusion protein (Na(+)/drug antiporter) MATE-like MDR efflux pump
B: Multi antimicrobial extrusion protein (Na(+)/drug antiporter) MATE-like MDR efflux pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6934
Polymers99,5222
Non-polymers1712
Water00
1
A: Multi antimicrobial extrusion protein (Na(+)/drug antiporter) MATE-like MDR efflux pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8472
Polymers49,7611
Non-polymers851
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Multi antimicrobial extrusion protein (Na(+)/drug antiporter) MATE-like MDR efflux pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8472
Polymers49,7611
Non-polymers851
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)159.800, 241.850, 46.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Multi antimicrobial extrusion protein (Na(+)/drug antiporter) MATE-like MDR efflux pump


Mass: 49761.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: N16961 / Gene: NorM / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: C3NQD8
#2: Chemical ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Rb

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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: 4.48 Å3/Da / Density % sol: 72.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 50mM Tris-HCl pH 7.2-8.6, 87 mM (NH4)2SO4, and 16-24% polyethylene glycol 250 dimethyl ether in D2O, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0093 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 4→20 Å / Num. obs: 13531 / Biso Wilson estimate: -12.2 Å2

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Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→20 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 2790903.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.342 683 5 %RANDOM
Rwork0.309 ---
obs0.309 13531 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 12.1578 Å2 / ksol: 0.1 e/Å3
Displacement parametersBiso mean: 118.4 Å2
Baniso -1Baniso -2Baniso -3
1-63.47 Å20 Å20 Å2
2---91.48 Å20 Å2
3---28.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.94 Å0.79 Å
Luzzati d res low-20 Å
Luzzati sigma a0.9 Å0.88 Å
Refinement stepCycle: LAST / Resolution: 4.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7011 0 2 0 7013
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d1.34
X-RAY DIFFRACTIONc_mcbond_it19.811.5
X-RAY DIFFRACTIONc_mcangle_it30.672
X-RAY DIFFRACTIONc_scbond_it24.312
X-RAY DIFFRACTIONc_scangle_it34.342.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 4.2→4.46 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 96 4.4 %
Rwork0.404 2080 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2RB.paramRB.top

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