Bioisis

"MnmE bound to GppNHp"

Experimental SAS Curve

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Low_res_thumbnail

Experimental Mass

109,000 Da

Experimental Details for BID:  MNME3P
Experiment ID: 108
Collected at: X33 DESY, Hamburg Germany
Contributors: Fislage, M ,  Brosens, E ,  Garcia-pino, A ,  Versees, W
SAXS data of E. coli MnmE bound to GppNHp. 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 GppNHp. Sample homogeneity was assessed using SEC-MALS.
single concentration

Electron Pair Distribution

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       Dmax → 136 Å


Guinier Plot

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     Guinier Rg → 37.4 Å

Real Space Rg → 39.6 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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MnmE is in its GppNHp bound state in equilibrium between the open and the closed conformation

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.


No Model

No structural model was used to interpret the SAXS data, please read the following:

SAXS data of E. coli MnmE bound to GppNHp. 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 GppNHp. Sample homogeneity was assessed using SEC-MALS.


Additional Experimental Details
Title

MnmE bound to GppNHp

Description

SAXS data of E. coli MnmE bound to GppNHp. 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 GppNHp. Sample homogeneity was assessed using SEC-MALS.

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)