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- PDB-6iia: MexB in complex with LMNG -

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Basic information

Entry
Database: PDB / ID: 6iia
TitleMexB in complex with LMNG
ComponentsMultidrug resistance protein MexBMultiple drug resistance
KeywordsMEMBRANE PROTEIN / multidrug / transporter
Function / homology
Function and homology information


xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / transmembrane transport / response to antibiotic / plasma membrane
Similarity search - Function
Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family
Similarity search - Domain/homology
Lauryl Maltose Neopentyl Glycol / Multidrug resistance protein MexB
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsNakashima, R. / Sakurai, K. / Nakao, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR12M6 Japan
CitationJournal: Sci Rep / Year: 2019
Title: Crystal structures of multidrug efflux pump MexB bound with high-molecular-mass compounds.
Authors: Sakurai, K. / Yamasaki, S. / Nakao, K. / Nishino, K. / Yamaguchi, A. / Nakashima, R.
History
DepositionOct 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Dec 13, 2023Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multidrug resistance protein MexB
B: Multidrug resistance protein MexB
C: Multidrug resistance protein MexB
D: Multidrug resistance protein MexB
E: Multidrug resistance protein MexB
F: Multidrug resistance protein MexB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)684,2468
Polymers682,2366
Non-polymers2,0102
Water0
1
A: Multidrug resistance protein MexB
B: Multidrug resistance protein MexB
C: Multidrug resistance protein MexB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,1234
Polymers341,1183
Non-polymers1,0051
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19350 Å2
ΔGint-80 kcal/mol
Surface area107770 Å2
MethodPISA
2
D: Multidrug resistance protein MexB
E: Multidrug resistance protein MexB
F: Multidrug resistance protein MexB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,1234
Polymers341,1183
Non-polymers1,0051
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19320 Å2
ΔGint-87 kcal/mol
Surface area108570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.949, 134.343, 149.692
Angle α, β, γ (deg.)87.530, 70.200, 89.020
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Multidrug resistance protein MexB / Multiple drug resistance / Multidrug-efflux transporter MexB


Mass: 113706.008 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: mexB, PA0426 / Production host: Escherichia coli (E. coli) / References: UniProt: P52002
#2: Chemical ChemComp-AV0 / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside / 2-decyl-2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]methyl}dodecyl4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside


Mass: 1005.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H88O22

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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: 3.48 Å3/Da / Density % sol: 64.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 50mM Na Acetate-HCl pH5.0, 300mM NaCl, 25% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→140.73 Å / Num. obs: 199569 / % possible obs: 98.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.033 / Rrim(I) all: 0.066 / Χ2: 0.838 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.953.90.753100110.7860.4410.8730.92898.7
2.95-33.90.66199840.820.3860.7650.94398.8
3-3.063.90.566100000.8480.330.6550.92798.7
3.06-3.123.90.45699480.8940.2650.5280.9498.7
3.12-3.1940.37699420.9170.2180.4340.94199
3.19-3.2740.30799870.940.1780.3550.94299
3.27-3.3540.256100010.9530.1480.2960.94198.9
3.35-3.4440.19299690.9730.1110.2220.94999
3.44-3.543.90.15100020.9810.0870.1740.97599
3.54-3.6540.11499700.9880.0660.1320.91199.1
3.65-3.783.90.08699970.9920.050.10.91799
3.78-3.943.90.064100220.9940.0370.0740.91299.1
3.94-4.113.90.045100170.9960.0260.0530.83299.2
4.11-4.333.90.03699770.9970.0210.0420.80699.3
4.33-4.63.90.028100570.9970.0160.0320.78299.3
4.6-4.963.90.024100110.9980.0140.0280.75199.3
4.96-5.463.90.022100370.9980.0130.0260.66299.5
5.46-6.253.80.022100280.9970.0130.0250.60999.5
6.25-7.873.80.015100690.9990.0090.0180.52499.5
7.87-1003.60.01295400.9990.0070.0140.48194.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W9I

3w9i


Resolution: 2.91→140.73 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.863 / SU B: 17.911 / SU ML: 0.342 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.437
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 9196 5 %RANDOM
Rwork0.2339 ---
obs0.2361 174254 92.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 202.55 Å2 / Biso mean: 54.214 Å2 / Biso min: 10.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å21.18 Å2-0.48 Å2
2---0.22 Å20.44 Å2
3---0.32 Å2
Refinement stepCycle: final / Resolution: 2.91→140.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46738 0 138 0 46876
Biso mean--48.62 --
Num. residues----6160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01947831
X-RAY DIFFRACTIONr_bond_other_d0.0060.0246802
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9765000
X-RAY DIFFRACTIONr_angle_other_deg1.0983107467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08856151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.62924.3951859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.743157908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2715228
X-RAY DIFFRACTIONr_chiral_restr0.0890.27612
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02154121
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0210603
LS refinement shellResolution: 2.909→2.984 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 450 -
Rwork0.297 8576 -
all-9026 -
obs--61.43 %

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