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- PDB-6wk5: Crystal structure of Gdx-Clo from Small Multidrug Resistance fami... -

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Basic information

Entry
Database: PDB / ID: 6wk5
TitleCrystal structure of Gdx-Clo from Small Multidrug Resistance family of transporters
Components
  • L10 monobody
  • Multidrug resistance protein, SMR family
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 / 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: 3.5 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 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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


Theoretical massNumber of molelcules
Total (without water)42,9234
Polymers42,9234
Non-polymers00
Water00
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 details see https://www.pnas.org/content/pnas/115/12/3060.full.pdf
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.800, 51.093, 108.433
Angle α, β, γ (deg.)90.000, 93.080, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Multidrug resistance protein, SMR family


Mass: 11529.445 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)
Has ligand of interestY
Has protein modificationY

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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: 4.34 Å3/Da / Density % sol: 71.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.1 M LiNO3, 0.1 M N-(2-Acetamido)iminodiacetic acid (ADA) pH 6.8, and 35% PEG 600

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.5→54.14 Å / Num. obs: 10080 / % possible obs: 99.97 % / Redundancy: 7.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.035 / Rrim(I) all: 0.07 / Net I/σ(I): 17.3
Reflection shellResolution: 3.5→3.83 Å / Rmerge(I) obs: 0.148 / Num. unique obs: 2389 / CC1/2: 0.995 / Rpim(I) all: 0.086 / Rrim(I) all: 0.171

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.25data extraction
PHENIX1.17.1_3660refinement
SHARPphasing
Aimlessdata scaling
DIALSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 3.5→44.23 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 33.78
RfactorNum. reflection% reflection
Rfree0.2858 512 5.08 %
Rwork0.2516 --
obs0.2534 10071 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 243.2 Å2 / Biso mean: 101.9386 Å2 / Biso min: 62.72 Å2
Refinement stepCycle: final / Resolution: 3.5→44.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2953 0 0 0 2953
Num. residues----384
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.5-3.850.37341310.2723642495
3.85-4.410.29241260.253123612487
4.41-5.550.25551220.23723772499
5.55-44.230.28271330.25524572590

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