Bioisis

"MnmE bound to GDP-AlFx"

Experimental SAS Curve

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Experimental Mass

121,000 Da

Experimental Details for BID:  MNME2P
Experiment ID: 110
Collected at: X33 DESY, Hamburg Germany
Contributors: Fislage, M ,  Brosens, E ,  Garcia-pino, A ,  Versees, W
SAXS data of E. coli MnmE bound to GDP-AlFx. MnmE was expressed in E. coli and purified via Ni-NTA affinity chromatography followed by the removal of bound nucleotides using alkaline phosphatase. Subsequently MnmE was purified via a second Ni-NTA affinity chromatography and gel filtration. MnmE was measured in the presence of 1 mM GDP-AlFx. Sample homogeneity was assesed using SEC-MALS and DLS.
single concentration

Electron Pair Distribution

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       Dmax → 138 Å


Guinier Plot

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     Guinier Rg → 37.2 Å

Real Space Rg → 37.8 Å

The Guinier plot is used to estimate the radius of gyration, Rg, which is taken from the slope of a line observed at low scattering angles (typically in the range where q* Rg < 1.3). This should be in reasonable agreement with the real space Rg.


Kratky Plot

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The Kratky plot can be used to visually assess the degree of "unfoldedness" of a protein or RNA sample. The plot of a well-behaved folded protein approaches the baseline at high q values creating a parabolic shape.


PDB Model fit to SAXS Data

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The red line is the calculated SAXS profile from a PDB model scaled to the experimental SAXS curve (cyan). The two curves agree with a Chi2 of 2.4.


Additional Experimental Details
Title

MnmE bound to GDP-AlFx

Description

SAXS data of E. coli MnmE bound to GDP-AlFx. MnmE was expressed in E. coli and purified via Ni-NTA affinity chromatography followed by the removal of bound nucleotides using alkaline phosphatase. Subsequently MnmE was purified via a second Ni-NTA affinity chromatography and gel filtration. MnmE was measured in the presence of 1 mM GDP-AlFx. Sample homogeneity was assesed using SEC-MALS and DLS.

Publication

SAXS analysis of the tRNA-modifying enzyme complex MnmE/MnmG reveals a novel interaction mode and GTP-induced oligomerization, Fislage M, et al., Nucleic Acids Res. 2014;42(9):5978-92. doi: 10.1093/nar/gku213. Epub 2014 Mar 14.,PMID: 24634441

Contributors

Fislage, M ,  Brosens, E ,  Garcia-pino, A ,  Versees, W

Genomics and Proteomics

The experiment is composed of a single gene/ORF

Abbreviated name: EcMnmE

Annotation: E. coli MnmE, GTPase involved in tRNA modification

MSDNDTIVAQ ATPPGRGGVG ILRISGFKAR EVAETVLGKL PKPRYADYLP FKDADGSVLD QGIALWFPGP NSFTGEDVLE LQGHGGPVIL DLLLKRILTI PGLRIARPGE FSERAFLNDK LDLAQAEAIA DLIDASSEQA ARSALNSLQG AFSARVNHLV EALTHLRIYV EAAIDFPDEE IDFLSDGKIE AQLNDVIADL DAVRAEARQG SLLREGMKVV IAGRPNAGKS SLLNALAGRE AAIVTDIAGT TRDVLREHIH IDGMPLHIID TAGLREASDE VERIGIERAW QEIEQADRVL FMVDGTTTDA VDPAEIWPEF IARLPAKLPI TVVRNKADIT GETLGMSEVN GHALIRLSAR TGEGVDVLRN HLKQSMGFDT NMEGGFLARR RHLQALEQAA EHLQQGKAQL LGAWAGELLA EELRLAQQNL SEITGEFTSD DLLGRIFSSF CIGK
categoryamino acid composition(%)
HydrophobicI(7.3) V(5.5) L(12.1) M(1.5) A(11.9) G(9.0) P(3.7)
AromaticF(3.5) W(0.9) Y(0.7)
HydrophilicR(7.0) K(3.1) E(7.9) D(7.3) Q(4.0) N(2.9) H(2.2) S(4.8) T(4.4) C(0.2)