- PDB-6wk8: Crystal structure of Gdx-Clo from Small Multidrug Resistance fami... -
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Basic information
Entry
Database: PDB / ID: 6wk8
Title
Crystal structure of Gdx-Clo from Small Multidrug Resistance family of transporters in complex with phenylguanidinium
Components
L10 monobody
Multidrug resistance protein, SMR family
Keywords
TRANSPORT PROTEIN / Small Multidrug Resistance / guanidinium transporter / EmrE homologue / dual topology protein
Function / homology
Small 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 species
Clostridiales bacterium oral taxon 876 str. F0540 (bacteria) Homo sapiens (human)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.53 Å
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)
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
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 number
5
Space group name H-M
C121
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Components
#1: Protein
Multidrugresistanceprotein, SMRfamily
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
L10monobody
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)
Method 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
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.3093
468
4.9 %
RANDOM
Rwork
0.2571
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obs
0.2596
9018
36.53 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
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