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- SASDBC9: GDP bound form of C-terminal deletion mutant of ObgE from E.coli ... -

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ID or keywords:

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Basic information

Entry
Database: SASBDB / ID: SASDBC9
SampleGDP bound form of C-terminal deletion mutant of ObgE from E.coli (ObgE_340 with GDP)
  • GTPase ObgE/CgtA (protein), ObgE_340, Escherichia coli (strain K12)
Function / homology
Function and homology information


guanyl ribonucleotide binding / dormancy process / negative regulation of ribosome biogenesis / guanosine tetraphosphate binding / ribosomal large subunit binding / ribosome assembly / chromosome segregation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GDP binding / rRNA binding ...guanyl ribonucleotide binding / dormancy process / negative regulation of ribosome biogenesis / guanosine tetraphosphate binding / ribosomal large subunit binding / ribosome assembly / chromosome segregation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GDP binding / rRNA binding / GTPase activity / GTP binding / magnesium ion binding / DNA binding / cytosol
Similarity search - Function
GTP1/OBG, conserved site / GTP1/OBG family signature. / OBG-type GTPase / GTP1/OBG domain / GTP-binding protein Obg/CgtA / GTP1/OBG domain superfamily / GTP1/OBG / Obg domain profile. / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. ...GTP1/OBG, conserved site / GTP1/OBG family signature. / OBG-type GTPase / GTP1/OBG domain / GTP-binding protein Obg/CgtA / GTP1/OBG domain superfamily / GTP1/OBG / Obg domain profile. / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesEscherichia coli (strain K12) (bacteria)
CitationDate: 2017 Feb 21
Title: Structural and Biochemical Analysis of Escherichia coli ObgE, a Central Regulator of Bacterial Persistence
Authors: Gkekas S / Singh R / Shkumatov A / Messens J / Fauvart M / Verstraeten N / Michiels J
Contact author
  • Alexander V. Shkumatov (VUB, Vrije Universiteit Brussel, Pleinlaan 2 1050 Brussel)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Models

Model #1118
Type: dummy / Software: DAMMIN (v2.7.2) / Radius of dummy atoms: 2.50 A / Symmetry: P1
Comment: Average model generated by DAMAVER and used as a starting model for refinement with DAMMIN (r7897M)
Chi-square value: 0.606 / P-value: 0.531000
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: GDP bound form of C-terminal deletion mutant of ObgE from E.coli (ObgE_340 with GDP)
Specimen concentration: 1.00-8.00
BufferName: 20 mM Hepes, 300 mM NaCl, 250 mM imidazole, 5 mM MgCl2, 2 mM DTT, 400 uM GDP
pH: 7.5
Entity #421Name: ObgE_340 / Type: protein / Description: GTPase ObgE/CgtA / Formula weight: 38.899 / Num. of mol.: 1 / Source: Escherichia coli (strain K12) / References: UniProt: P42641
Sequence: MGSSHHHHHH SSGLVPRGSH MKFVDEASIL VVAGDGGNGC VSFRREKYIP KGGPDGGDGG DGGDVWMEAD ENLNTLIDYR FEKSFRAERG QNGASRDCTG KRGKDVTIKV PVGTRVIDQG TGETMGDMTK HGQRLLVAKG GWHGLGNTRF KSSVNRTPRQ KTNGTPGDKR ...Sequence:
MGSSHHHHHH SSGLVPRGSH MKFVDEASIL VVAGDGGNGC VSFRREKYIP KGGPDGGDGG DGGDVWMEAD ENLNTLIDYR FEKSFRAERG QNGASRDCTG KRGKDVTIKV PVGTRVIDQG TGETMGDMTK HGQRLLVAKG GWHGLGNTRF KSSVNRTPRQ KTNGTPGDKR ELLLELMLLA DVGMLGMPNA GKSTFIRAVS AAKPKVADYP FTTLVPSLGV VRMDNEKSFV VADIPGLIEG AAEGAGLGIR FLKHLERCRV LLHLIDIDPI DGTDPVENAR IIISELELYS QDLATKPRWL VFNKIDLLDK VEAEEKAKAI AEALGWEDKY YLISAASGLG VKDLCWDVMT FIIENPVA

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Experimental information

BeamInstrument name: Rigaku BioSAXS-2000 / City: Brussels / 国: Belgium / Type of source: X-ray in house / Wavelength: 1.54 Å / Dist. spec. to detc.: 1 mm
DetectorName: Pilatus 100K / Pixsize x: 172 mm
Scan
Title: GDP bound form of C-terminal deletion mutant of ObgE from E.coli (ObgE_340 with GDP)
Measurement date: Feb 1, 2015 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 1800 sec. / Number of frames: 3 / Unit: 1/A /
MinMax
Q0.008 0.6829
Distance distribution function P(R)
Sofotware P(R): GNOM 4.6 / Number of points: 461 /
MinMax
Q0.02099 0.6829
P(R) point10 470
R0 111
Result
Type of curve: merged /
ExperimentalPorod
MW39.1 kDa41.5 kDa
Volume-70673 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I01.04 0.01 1.01 0.01
Radius of gyration, Rg3.17 nm0.4 2.95 nm0.04

MinMaxError
D-11 1
Guinier point14 26 -

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