[English] 日本語
Yorodumi
- PDB-8bft: The E. coli TrpD2 protein YbiB in complex with a C-terminal pepti... -

+
Open data


ID or keywords:

Loading...

-
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 / anthranilate phosphoribosyltransferase activity / dormancy process / negative regulation of ribosome biogenesis / L-tryptophan biosynthetic process / guanosine tetraphosphate binding / ribosomal large subunit binding / ribosome assembly / chromosome segregation / GDP binding ...guanyl ribonucleotide binding / anthranilate phosphoribosyltransferase activity / dormancy process / negative regulation of ribosome biogenesis / L-tryptophan biosynthetic process / guanosine tetraphosphate binding / ribosomal large subunit binding / ribosome assembly / chromosome segregation / GDP binding / ribosomal large subunit assembly / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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. / GTP1/OBG domain / GTP-binding protein Obg/CgtA / GTP1/OBG domain superfamily / OBG-type GTPase / GTP1/OBG / Obg domain profile. / Anthranilate phosphoribosyl transferase / Glycosyl transferase family 3, N-terminal domain ...GTP1/OBG, conserved site / GTP1/OBG family signature. / GTP1/OBG domain / GTP-binding protein Obg/CgtA / GTP1/OBG domain superfamily / OBG-type GTPase / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more