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- PDB-6wk8: Crystal structure of Gdx-Clo from Small Multidrug Resistance fami... -

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Basic information

Entry
Database: PDB / ID: 6wk8
TitleCrystal structure of Gdx-Clo from Small Multidrug Resistance family of transporters in complex with phenylguanidinium
Components
  • L10 monobody
  • Multidrug resistance protein, SMR familyMultiple drug resistance
KeywordsTRANSPORT PROTEIN / Small Multidrug Resistance / guanidinium transporter / EmrE homologue / dual topology protein
Function / homologySmall drug/metabolite transporter protein family / Small multidrug resistance protein / Small Multidrug Resistance protein / transmembrane transporter activity / plasma membrane / Dodecyldimethylphosphine oxide / 1-phenylguanidine / 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: 2.53 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4127
Polymers42,5484
Non-polymers8643
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, We observe a single dominant peak on the FPLC chromatogram corresponding to a Gdx-Clo dimer, cross-linking, For further information see Kermani, et al. Guanidinium export is ...Evidence: gel filtration, We observe a single dominant peak on the FPLC chromatogram corresponding to a Gdx-Clo dimer, cross-linking, For further information see Kermani, et al. Guanidinium export is the primal function of SMR family transporters. Proceedings of the National Academy of Sciences 115, 3060-3065 (2018)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.819, 50.507, 108.575
Angle α, β, γ (deg.)90.000, 92.180, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 11341.865 Da / Num. of mol.: 2
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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-PL0 / 1-phenylguanidine


Mass: 135.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-9PD / Dodecyldimethylphosphine oxide / APO-12


Mass: 246.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H31OP
#5: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
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: 4.3 Å3/Da / Density % sol: 71.42 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 100 mM LiNaSO4, 0.1 M Tris pH 8.75, 34% PEG 600 / PH range: 8.75

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.5→59 Å / Num. obs: 9466 / % possible obs: 85 % / Redundancy: 7.1 % / CC1/2: 0.946 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.057 / Rrim(I) all: 0.145 / Net I/σ(I): 6.4
Reflection shellResolution: 2.5→3 Å / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 473 / CC1/2: 0.807 / Rpim(I) all: 0.438 / Rrim(I) all: 0.723

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIXv5.0refinement
SHELXphasing
SHARPphasing
STARANISOdata scaling
DIALSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.53→58.39 Å / Cor.coef. Fo:Fc: 0.85 / Cor.coef. Fo:Fc free: 0.77 / SU B: 11.895 / SU ML: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.644
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3093 468 4.9 %RANDOM
Rwork0.2571 ---
obs0.2596 9018 36.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 176.24 Å2 / Biso mean: 52.447 Å2 / Biso min: 27.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20.69 Å2
2---0.19 Å20 Å2
3---0.51 Å2
Refinement stepCycle: final / Resolution: 2.53→58.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2959 0 51 0 3010
Biso mean--75.66 --
Num. residues----385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133092
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172995
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.654233
X-RAY DIFFRACTIONr_angle_other_deg1.1881.5846901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2325381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54621.2596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73615471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.561158
X-RAY DIFFRACTIONr_chiral_restr0.0570.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023336
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02660
LS refinement shellResolution: 2.533→2.598 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.584 3 -
Rwork0.326 40 -
all-43 -
obs--2.28 %

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