[English] 日本語
Yorodumi
- PDB-8bfr: The E. coli TrpD2 protein YbiB at 1.3 A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bfr
TitleThe E. coli TrpD2 protein YbiB at 1.3 A resolution
ComponentsProtein YbiB
KeywordsDNA BINDING PROTEIN / TrpD2 / YbiB / DNA-binding
Function / homology
Function and homology information


anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / protein homodimerization activity / DNA binding / RNA binding / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Uncharacterized protein YbiB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7373
Polymers37,5531
Non-polymers1842
Water7,404411
1
A: Protein YbiB
hetero molecules

A: Protein YbiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4756
Polymers75,1062
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3010 Å2
ΔGint-20 kcal/mol
Surface area25530 Å2
Unit cell
Length a, b, c (Å)134.154, 64.004, 47.496
Angle α, β, γ (deg.)90.000, 97.220, 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 (E. coli) / References: UniProt: P30177
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.2, 15 % w/v PEG 3350

-
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: 1.3→66.55 Å / Num. obs: 80496 / % possible obs: 93.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 12.62 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.8
Reflection shellResolution: 1.3→1.397 Å / Num. unique obs: 4026 / CC1/2: 0.624

-
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: 4MUO

4muo


Resolution: 1.3→66.55 Å / SU ML: 0.0932 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.5406
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1667 3975 4.94 %
Rwork0.135 76516 -
obs0.1366 80491 82.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.61 Å2
Refinement stepCycle: LAST / Resolution: 1.3→66.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 12 411 2849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00932539
X-RAY DIFFRACTIONf_angle_d1.08683459
X-RAY DIFFRACTIONf_chiral_restr0.0788390
X-RAY DIFFRACTIONf_plane_restr0.0097459
X-RAY DIFFRACTIONf_dihedral_angle_d6.8991367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.3811170.309234X-RAY DIFFRACTION7.28
1.32-1.330.2966240.2677360X-RAY DIFFRACTION11.02
1.33-1.350.3251240.2468467X-RAY DIFFRACTION14.17
1.35-1.370.3389450.27760X-RAY DIFFRACTION23.11
1.37-1.390.3174560.25041237X-RAY DIFFRACTION37.62
1.39-1.410.272930.23561763X-RAY DIFFRACTION53.26
1.41-1.430.28471320.2212333X-RAY DIFFRACTION70.25
1.43-1.450.24381470.212867X-RAY DIFFRACTION86.88
1.45-1.480.2431560.19473224X-RAY DIFFRACTION96.93
1.48-1.510.20411690.18143276X-RAY DIFFRACTION99.45
1.51-1.540.20981680.16373340X-RAY DIFFRACTION99.94
1.54-1.570.20561720.15263299X-RAY DIFFRACTION99.91
1.57-1.60.18941830.14463318X-RAY DIFFRACTION100
1.6-1.640.16371550.14213338X-RAY DIFFRACTION99.94
1.64-1.680.17231680.13793307X-RAY DIFFRACTION100
1.68-1.720.15831700.13173310X-RAY DIFFRACTION100
1.72-1.770.17221780.13143358X-RAY DIFFRACTION100
1.77-1.830.17971620.13563284X-RAY DIFFRACTION100
1.83-1.90.18811790.12413353X-RAY DIFFRACTION99.97
1.9-1.970.1511740.1173295X-RAY DIFFRACTION99.97
1.97-2.060.15241850.11313331X-RAY DIFFRACTION99.97
2.06-2.170.14151720.12093309X-RAY DIFFRACTION99.97
2.17-2.310.15262060.11423306X-RAY DIFFRACTION99.94
2.31-2.490.13491460.11953378X-RAY DIFFRACTION100
2.49-2.740.14371570.12083350X-RAY DIFFRACTION99.97
2.74-3.130.13751690.12433332X-RAY DIFFRACTION100
3.13-3.950.14361740.11993384X-RAY DIFFRACTION99.97
3.95-66.550.18141940.14823403X-RAY DIFFRACTION99.89

+
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