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- PDB-8vxu: Crystal structure of Gdx-Clo A60T from Small Multidrug Resistance... -

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Basic information

Entry
Database: PDB / ID: 8vxu
TitleCrystal structure of Gdx-Clo A60T from Small Multidrug Resistance family of transporters in complex with cetyltrimetylammonium
Components
  • L10 Monobody
  • Multidrug resistance protein, SMR familyMultiple drug resistance
KeywordsTRANSPORT PROTEIN / Small Multidrug Resistance / SMR / quaternary ammonium
Function / homologySmall drug/metabolite transporter protein family / Small multidrug resistance protein / Small Multidrug Resistance protein / transmembrane transporter activity / plasma membrane / CETYL-TRIMETHYL-AMMONIUM / Multidrug resistance protein, SMR family
Function and homology information
Biological speciesClostridia bacterium (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsBurata, O.E. / Stockbridge, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1845012 United States
CitationJournal: To Be Published
Title: Peripheral mutations underlie promiscuous transport of quaternary ammonium antiseptics by Small Multidrug Resistance transporters
Authors: Burata, O.E. / Stockbridge, R.B.
History
DepositionFeb 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multidrug resistance protein, SMR family
B: Multidrug resistance protein, SMR family
C: Multidrug resistance protein, SMR family
D: Multidrug resistance protein, SMR family
E: L10 Monobody
F: L10 Monobody
H: L10 Monobody
G: L10 Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,61912
Polymers86,4818
Non-polymers1,1384
Water0
1
A: Multidrug resistance protein, SMR family
B: Multidrug resistance protein, SMR family
E: L10 Monobody
G: L10 Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8096
Polymers43,2404
Non-polymers5692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Multidrug resistance protein, SMR family
D: Multidrug resistance protein, SMR family
F: L10 Monobody
H: L10 Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8096
Polymers43,2404
Non-polymers5692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.132, 74.873, 108.252
Angle α, β, γ (deg.)93.27, 89.93, 109.51
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Multidrug resistance protein, SMR family / Multiple drug resistance


Mass: 11787.357 Da / Num. of mol.: 4 / Mutation: A60T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridia bacterium (bacteria) / Gene: sugE / Plasmid: pET21b/sugE_Clo
Details (production host): IPTG-induced, Ampicillin Resistance
Cell line (production host): Keio / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): E. coli C41(DE3) / Variant (production host): C41 / References: UniProt: U2EQ00
#2: Antibody
L10 Monobody


Mass: 9832.803 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET21b/L10_Mb
Details (production host): T7, Kanamycin resistant, IPTG inducible
Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-16A / CETYL-TRIMETHYL-AMMONIUM


Mass: 284.543 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H42N / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 4.42 Å3/Da / Density meas: 0.335 Mg/m3 / Density % sol: 72.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.75
Details: 100 mM CaCl2, 100 mM N-(2-acetamido)iminodiacetic acid (ADA) pH 6.75, and 33% PEG 600

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 2.29→70.5 Å / Num. obs: 22068 / % possible obs: 82.1 % / Redundancy: 3.8 % / CC1/2: 0.98 / Net I/σ(I): 6.2
Reflection shellResolution: 2.29→2.75 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1160 / CC1/2: 0.614 / % possible all: 68.9

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
DIALSdata collection
STARANISOdata scaling
PHASERphasing
DIALS3.17.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→35.22 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / Phase error: 37.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.289 1153 5.22 %
Rwork0.2773 --
obs0.2779 22068 32.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.36 Å2
Refinement stepCycle: LAST / Resolution: 2.29→35.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5896 0 57 0 5953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.667
X-RAY DIFFRACTIONf_dihedral_angle_d12.7312089
X-RAY DIFFRACTIONf_chiral_restr0.0451013
X-RAY DIFFRACTIONf_plane_restr0.005968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.390.158610.393961X-RAY DIFFRACTION1
2.39-2.520.4346170.3799258X-RAY DIFFRACTION3
2.52-2.670.2965320.3719495X-RAY DIFFRACTION6
2.67-2.880.4605540.3709812X-RAY DIFFRACTION10
2.88-3.170.4269880.37281464X-RAY DIFFRACTION19
3.17-3.630.33061970.3313634X-RAY DIFFRACTION46
3.63-4.570.29763890.27496997X-RAY DIFFRACTION88
4.57-35.220.2533750.25397194X-RAY DIFFRACTION90

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