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- PDB-5m04: Structure of ObgE from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 5m04
TitleStructure of ObgE from Escherichia coli
ComponentsGTPase ObgE/CgtA
KeywordsHYDROLASE / GTPase / ObgE / CgtA
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
Spo0b-associated Gtp-binding Protein; Chain: A, / GTP1/OBG domain / 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. ...Spo0b-associated Gtp-binding Protein; Chain: A, / GTP1/OBG domain / 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 / Distorted Sandwich / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTPase ObgE/CgtA
Similarity search - Component
Biological speciesEscherichia coli DH5[alpha] (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGkekas, S. / Singh, R.K. / Versees, W.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Fonds voor Wetenschappelijk Onderzoek (FWO)G.0471.12N, G0B2515N Belgium
Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT). Belgium
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural and biochemical analysis of Escherichia coli ObgE, a central regulator of bacterial persistence.
Authors: Gkekas, S. / Singh, R.K. / Shkumatov, A.V. / Messens, J. / Fauvart, M. / Verstraeten, N. / Michiels, J. / Versees, W.
History
DepositionOct 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTPase ObgE/CgtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6663
Polymers39,1991
Non-polymers4682
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-11 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.590, 83.000, 177.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein GTPase ObgE/CgtA / GTP-binding protein Obg


Mass: 39198.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DH5[alpha] (bacteria) / Gene: obgE, cgtA, obg, yhbZ, b3183, JW3150 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta, pLysS
References: UniProt: P42641, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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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: 3.24 Å3/Da / Density % sol: 62.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 16% (w/v) polyethylene glycol (PEG) 6000, 15% (v/v) 2-propanol and 100 mM Sodium Citrate/HCl pH 5.6.
PH range: 5.4.-5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.07812 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 1.85→88.73 Å / Num. obs: 41090 / % possible obs: 99.9 % / Redundancy: 6.81 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09028 / Rrim(I) all: 0.09784 / Net I/σ(I): 9.67
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 6.97 % / Rmerge(I) obs: 2.326 / Mean I/σ(I) obs: 1 / CC1/2: 0.489 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LNZ

1lnz


Resolution: 1.85→88.73 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.944 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.119
RfactorNum. reflection% reflectionSelection details
Rfree0.23881 2051 5 %RANDOM
Rwork0.19801 ---
obs0.20007 39039 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.784 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2--1.25 Å20 Å2
3----0.58 Å2
Refinement stepCycle: 1 / Resolution: 1.85→88.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 29 169 2768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192620
X-RAY DIFFRACTIONr_bond_other_d0.0020.022529
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.9883544
X-RAY DIFFRACTIONr_angle_other_deg0.99635827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7935336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6424.486107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58715451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3421516
X-RAY DIFFRACTIONr_chiral_restr0.1020.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212955
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02555
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8584.6661348
X-RAY DIFFRACTIONr_mcbond_other3.8584.6631347
X-RAY DIFFRACTIONr_mcangle_it5.4166.9761682
X-RAY DIFFRACTIONr_mcangle_other5.4166.9791683
X-RAY DIFFRACTIONr_scbond_it4.5335.1321272
X-RAY DIFFRACTIONr_scbond_other4.5425.1381264
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8727.4921850
X-RAY DIFFRACTIONr_long_range_B_refined9.61137.8032971
X-RAY DIFFRACTIONr_long_range_B_other9.55937.622922
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 150 -
Rwork0.354 2845 -
obs--99.7 %

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