[English] 日本語
Yorodumi
- PDB-6t5i: The Transcriptional Regulator PrfA from Listeria Monocytogenes in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t5i
TitleThe Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with inhibitor of WNT production (IWP)-2
ComponentsListeriolysin positive regulatory factor A
KeywordsTRANSCRIPTION / LISTERIA MONOCYTOGENES / DNA BINDING PROTEIN / INHIBITOR of WNT (IWP)
Function / homology
Function and homology information


positive regulation of single-species biofilm formation on inanimate substrate / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-9XK / Positive regulatory factor A
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOelker, M. / Grundstrom, C. / Blumenthal, A. / Sauer-Eriksson, A.E.
Funding support Sweden, Australia, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
National Health and Medical Research Council (Australia)GNT1142456 Australia
CitationJournal: Plos Pathog. / Year: 2022
Title: Inhibition of the master regulator of Listeria monocytogenes virulence enables bacterial clearance from spacious replication vacuoles in infected macrophages.
Authors: Tran, T.T. / Mathmann, C.D. / Gatica-Andrades, M. / Rollo, R.F. / Oelker, M. / Ljungberg, J.K. / Nguyen, T.T.K. / Zamoshnikova, A. / Kummari, L.K. / Wyer, O.J.K. / Irvine, K.M. / Melo- ...Authors: Tran, T.T. / Mathmann, C.D. / Gatica-Andrades, M. / Rollo, R.F. / Oelker, M. / Ljungberg, J.K. / Nguyen, T.T.K. / Zamoshnikova, A. / Kummari, L.K. / Wyer, O.J.K. / Irvine, K.M. / Melo-Bolivar, J. / Gross, A. / Brown, D. / Mak, J.Y.W. / Fairlie, D.P. / Hansford, K.A. / Cooper, M.A. / Giri, R. / Schreiber, V. / Joseph, S.R. / Simpson, F. / Barnett, T.C. / Johansson, J. / Dankers, W. / Harris, J. / Wells, T.J. / Kapetanovic, R. / Sweet, M.J. / Latomanski, E.A. / Newton, H.J. / Guerillot, R.J.R. / Hachani, A. / Stinear, T.P. / Ong, S.Y. / Chandran, Y. / Hartland, E.L. / Kobe, B. / Stow, J.L. / Sauer-Eriksson, A.E. / Begun, J. / Kling, J.C. / Blumenthal, A.
History
DepositionOct 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Listeriolysin positive regulatory factor A
B: Listeriolysin positive regulatory factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,28716
Polymers54,9152
Non-polymers1,37214
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-31 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.951, 92.667, 101.447
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Listeriolysin positive regulatory factor A / Listeriolysin positive regulatory protein / Listeriolysin regulatory protein / Pleitrophic ...Listeriolysin positive regulatory protein / Listeriolysin regulatory protein / Pleitrophic regulatory factor A / Positive regulatory factor A / PrfA / Transcriptional regulator


Mass: 27457.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: prfA, AJN46_04535, BWI22_01025 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4TVQ0
#2: Chemical ChemComp-9XK / ~{N}-(6-methyl-1,3-benzothiazol-2-yl)-2-[(4-oxidanylidene-3-phenyl-6,7-dihydrothieno[3,2-d]pyrimidin-2-yl)sulfanyl]ethanamide


Mass: 466.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18N4O2S3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Purified PrfA, in 200 mM NaCl and 20 mM NaP buffer at pH 6.5 was mixed with 1 mM IWP2 and 3.7 mM DTT prior to crystallization. Droplets of 1 microL protein solution at 3.1 mg ml-1 were mixed ...Details: Purified PrfA, in 200 mM NaCl and 20 mM NaP buffer at pH 6.5 was mixed with 1 mM IWP2 and 3.7 mM DTT prior to crystallization. Droplets of 1 microL protein solution at 3.1 mg ml-1 were mixed with 1 microL reservoir solution consisting of 29 % (w/v) PEG 4000, 100 mM sodium citrate pH 5.5, and 18 % (v/v) isopropanol. The dimethyl sulfoxide (DMSO) concentration was kept at 10% (v/v). Prior to vitrification, crystals were equilibrated for 2 days in a solution containing 35 % (w/v) PEG 4000, 100 mM sodium citrate pH 5.5 and 1 mM IWP-2.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2→46.4 Å / Num. obs: 30998 / % possible obs: 99.2 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.04 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 13.1 % / Rmerge(I) obs: 2.078 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3033 / CC1/2: 0.435 / Rpim(I) all: 0.609 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EUT
Resolution: 2→46.334 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.97
RfactorNum. reflection% reflection
Rfree0.2523 1550 5 %
Rwork0.1986 --
obs0.2012 30998 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 216.23 Å2 / Biso mean: 52.3169 Å2 / Biso min: 22.63 Å2
Refinement stepCycle: final / Resolution: 2→46.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3783 0 81 103 3967
Biso mean--62.4 47.37 -
Num. residues----464
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.06460.2971380.252261399
2.0646-2.13840.27381370.2401261299
2.1384-2.2240.28521380.2348262398
2.224-2.32520.26551380.2293262799
2.3252-2.44780.30291390.2387263799
2.4478-2.60110.29631390.2407265199
2.6011-2.80190.30391420.2271268899
2.8019-3.08390.26491400.2046266399
3.0839-3.530.27311420.1953270299
3.53-4.44680.21691460.16482751100
4.4468-46.3340.21921510.18552881100

+
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://pdbjlvh1.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