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- PDB-6wk9: Crystal structure of Gdx-Clo from Small Multidrug Resistance fami... -

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Basic information

Entry
Database: PDB / ID: 6wk9
TitleCrystal structure of Gdx-Clo from Small Multidrug Resistance family of transporters in complex with octylguanidinium
Components
  • L10 monobody
  • Multidrug resistance protein, SMR familyMultiple drug resistance
KeywordsTRANSPORT PROTEIN / Small Multidrug Resistance transporters / EmrE homologue / guanidinium transporter / dual topology protein
Function / homologySmall drug/metabolite transporter protein family / Small multidrug resistance protein / Small Multidrug Resistance protein / transmembrane transporter activity / plasma membrane / N-octylguanidine / Multidrug resistance protein, SMR family
Function and homology information
Biological speciesClostridiales bacterium oral taxon 876 str. F0540 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 Å
AuthorsKermani, A.A. / Stockbridge, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM128768 United States
CitationJournal: Nat Commun / Year: 2020
Title: The structural basis of promiscuity in small multidrug resistance transporters.
Authors: Kermani, A.A. / Macdonald, C.B. / Burata, O.E. / Ben Koff, B. / Koide, A. / Denbaum, E. / Koide, S. / Stockbridge, R.B.
History
DepositionApr 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,91023
Polymers85,0958
Non-polymers3,81415
Water97354
1
B: Multidrug resistance protein, SMR family
A: Multidrug resistance protein, SMR family
C: L10 monobody
D: L10 monobody
hetero molecules


  • defined by author
  • Evidence: gel filtration, We observe a single dominant peak on the FPLC chromatogram corresponding to a Gdx-Clo dimer, cross-linking, see the following paper for details: Kermani, et al. Guanidinium ...Evidence: gel filtration, We observe a single dominant peak on the FPLC chromatogram corresponding to a Gdx-Clo dimer, cross-linking, see the following paper for details: Kermani, et al. Guanidinium export is the primal function of SMR family transporters. Proceedings of the National Academy of Sciences 115, 3060-3065 (2018).
  • 44.5 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)44,54012
Polymers42,5484
Non-polymers1,9938
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Multidrug resistance protein, SMR family
E: Multidrug resistance protein, SMR family
G: L10 monobody
H: L10 monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,36911
Polymers42,5484
Non-polymers1,8227
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.042, 75.828, 109.123
Angle α, β, γ (deg.)92.540, 90.040, 109.630
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 11341.865 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridiales bacterium oral taxon 876 str. F0540 (bacteria)
Gene: HMPREF1982_00479 / Plasmid: pET-21c / Production host: Escherichia coli (E. coli) / References: UniProt: U2EQ00
#2: Antibody
L10 monobody


Mass: 9931.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#4: Chemical
ChemComp-U4G / N-octylguanidine


Mass: 171.283 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C9H21N3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
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: 4.72 Å3/Da / Density % sol: 73.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M calcium acetate, 0.1 M Hepes pH 7.5, 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: 0.9183 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9183 Å / Relative weight: 1
ReflectionResolution: 2.3→109 Å / Num. obs: 25091 / % possible obs: 85 % / Redundancy: 3.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.044 / Rrim(I) all: 0.088 / Net I/σ(I): 9.2
Reflection shellResolution: 2.3→2.7 Å / Rmerge(I) obs: 0.38 / Num. unique obs: 1255 / CC1/2: 0.913 / Rpim(I) all: 0.225 / Rrim(I) all: 0.442

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SHELXphasing
SHARPphasing
STARANISOdata reduction
DIALSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.32→33.01 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 41.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2859 1325 5.3 %
Rwork0.2457 23670 -
obs0.2478 24995 37.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.47 Å2 / Biso mean: 34.9191 Å2 / Biso min: 2.78 Å2
Refinement stepCycle: final / Resolution: 2.32→33.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5944 0 264 54 6262
Biso mean--50.75 28.99 -
Num. residues----774
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.32-2.410.473410.30362425
2.42-2.530.404100.3371161262
2.53-2.660.3072460.30525816279
2.66-2.830.3209690.30481166123517
2.83-3.040.29151020.30061646174824
3.04-3.350.3471610.2782551271237
3.35-3.830.28782050.25014572477765
3.83-4.830.28394370.22226592702995
4.83-33.010.26622940.24996422671691

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