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- PDB-8bft: The E. coli TrpD2 protein YbiB in complex with a C-terminal pepti... -

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Basic information

Entry
Database: PDB / ID: 8bft
TitleThe E. coli TrpD2 protein YbiB in complex with a C-terminal peptide from ObgE
Components
  • GTPase ObgE/CgtA
  • Protein YbiB
KeywordsDNA BINDING PROTEIN / TrpD2 / YbiB / ObgE / DNA-binding
Function / homology
Function and homology information


guanyl ribonucleotide binding / dormancy process / anthranilate phosphoribosyltransferase activity / negative regulation of ribosome biogenesis / tryptophan biosynthetic process / 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 ...guanyl ribonucleotide binding / dormancy process / anthranilate phosphoribosyltransferase activity / negative regulation of ribosome biogenesis / tryptophan biosynthetic process / 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 / protein homodimerization activity / DNA binding / RNA 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. / Anthranilate phosphoribosyl transferase / Glycosyl transferase family 3, N-terminal 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. / Anthranilate phosphoribosyl transferase / Glycosyl transferase family 3, N-terminal domain / Glycosyl transferase family 3, N-terminal domain superfamily / Glycosyl transferase family, helical bundle domain / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily / 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
DI(HYDROXYETHYL)ETHER / Uncharacterized protein YbiB / GTPase ObgE/CgtA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsDeckers, B. / Galicia, C. / Versees, W.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)11D4621N Belgium
Vrije Universiteit Brussel (Blegium)SRP50 Belgium
Research Foundation - Flanders (FWO)G0I1522N Belgium
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: YbiB: a novel interactor of the GTPase ObgE.
Authors: Deckers, B. / Vercauteren, S. / De Kock, V. / Martin, C. / Lazar, T. / Herpels, P. / Dewachter, L. / Verstraeten, N. / Peeters, E. / Ballet, S. / Michiels, J. / Galicia, C. / Versees, W.
History
DepositionOct 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein YbiB
B: GTPase ObgE/CgtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2644
Polymers40,0522
Non-polymers2122
Water6,936385
1
A: Protein YbiB
B: GTPase ObgE/CgtA
hetero molecules

A: Protein YbiB
B: GTPase ObgE/CgtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5288
Polymers80,1034
Non-polymers4244
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)133.469, 63.895, 47.416
Angle α, β, γ (deg.)90.000, 97.350, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Protein YbiB / TrpD2 / Anthranilate phosphoribosyltransferase 2


Mass: 37553.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ybiB, b0800, JW0785, trpD2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30177
#2: Protein/peptide GTPase ObgE/CgtA / GTP-binding protein Obg


Mass: 2498.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
References: UniProt: P42641, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citrate pH 5, 20% w/v PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.19→47.03 Å / Num. obs: 87511 / % possible obs: 92.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 13.81 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.4
Reflection shellResolution: 1.192→1.331 Å / Num. unique obs: 4374 / CC1/2: 0.696

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BFR

8bfr


Resolution: 1.19→47.03 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.5899
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1668 4256 4.86 %
Rwork0.1367 83249 -
obs0.1382 87505 69.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.78 Å2
Refinement stepCycle: LAST / Resolution: 1.19→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 0 14 385 2860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00922607
X-RAY DIFFRACTIONf_angle_d1.05143558
X-RAY DIFFRACTIONf_chiral_restr0.0733401
X-RAY DIFFRACTIONf_plane_restr0.0109475
X-RAY DIFFRACTIONf_dihedral_angle_d7.4718383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.2100.163411X-RAY DIFFRACTION0.26
1.21-1.220.405240.214252X-RAY DIFFRACTION1.38
1.22-1.230.275150.2315140X-RAY DIFFRACTION3.83
1.23-1.250.2306170.2337285X-RAY DIFFRACTION7.22
1.25-1.270.2732210.2281452X-RAY DIFFRACTION11.36
1.27-1.280.233360.2313623X-RAY DIFFRACTION15.68
1.28-1.30.243410.2142798X-RAY DIFFRACTION20.25
1.3-1.320.2248620.21711147X-RAY DIFFRACTION28.77
1.32-1.340.2407640.1971579X-RAY DIFFRACTION39.53
1.34-1.360.2374980.19971990X-RAY DIFFRACTION50.11
1.36-1.390.23621180.19442566X-RAY DIFFRACTION64.2
1.39-1.410.24361500.1833030X-RAY DIFFRACTION77
1.41-1.440.23151730.19323585X-RAY DIFFRACTION89.39
1.44-1.470.20731780.17613890X-RAY DIFFRACTION97.55
1.47-1.50.22052130.16853933X-RAY DIFFRACTION99.02
1.5-1.540.16791960.15823966X-RAY DIFFRACTION99.21
1.54-1.580.1892190.15643936X-RAY DIFFRACTION99.33
1.58-1.620.17862030.14683935X-RAY DIFFRACTION99.47
1.62-1.670.16921990.14073970X-RAY DIFFRACTION99.55
1.67-1.720.16932010.13453965X-RAY DIFFRACTION99.57
1.72-1.780.1772110.13383957X-RAY DIFFRACTION99.76
1.78-1.850.1662140.12893984X-RAY DIFFRACTION99.74
1.85-1.940.14891810.12484024X-RAY DIFFRACTION99.93
1.94-2.040.1532180.12193956X-RAY DIFFRACTION99.9
2.04-2.170.13742190.12043997X-RAY DIFFRACTION100
2.17-2.330.14361730.11993428X-RAY DIFFRACTION85.96
2.33-2.570.16412170.12444010X-RAY DIFFRACTION100
2.57-2.940.15732130.12694015X-RAY DIFFRACTION100
2.94-3.70.15132090.12573921X-RAY DIFFRACTION97.68
3.7-47.030.17561930.1444104X-RAY DIFFRACTION99.61

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