[English] 日本語
Yorodumi
- PDB-6qer: Apo Form Of ComR From S. Thermophilus in space group C2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qer
TitleApo Form Of ComR From S. Thermophilus in space group C2
ComponentsTranscriptional regulator
KeywordsTRANSCRIPTION / Quorum sensing / Competence / TPR domain / HTH DNA binding domain
Function / homology
Function and homology information


ComR, tetratricopeptide / ComR tetratricopeptide / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Transcriptional regulator
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.465 Å
AuthorsThuillier, J. / Nessler, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Molecular dissection of pheromone selectivity in the competence signaling system ComRS of streptococci.
Authors: Ledesma-Garcia, L. / Thuillier, J. / Guzman-Espinola, A. / Ensinck, I. / Li de la Sierra-Gallay, I. / Lazar, N. / Aumont-Nicaise, M. / Mignolet, J. / Soumillion, P. / Nessler, S. / Hols, P.
History
DepositionJan 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: 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
Revision 1.2Apr 22, 2020Group: 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 1.3Jan 24, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator
B: Transcriptional regulator
C: Transcriptional regulator
D: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)146,1924
Polymers146,1924
Non-polymers00
Water1,60389
1
A: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)36,5481
Polymers36,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)36,5481
Polymers36,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)36,5481
Polymers36,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)36,5481
Polymers36,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)271.790, 73.720, 78.310
Angle α, β, γ (deg.)90.00, 104.97, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Transcriptional regulator


Mass: 36547.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: cloning tag = GLGAGWSHPQFEK
Source: (gene. exp.) Streptococcus thermophilus (strain ATCC BAA-491 / LMD-9) (bacteria)
Strain: ATCC BAA-491 / LMD-9 / Gene: BN551_00358 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1L1QK15
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.05M Magnesium acetate 10% PEG8000 0.1M Sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980105 Å / Relative weight: 1
ReflectionResolution: 2.465→44.24 Å / Num. obs: 105306 / % possible obs: 99.59 % / Redundancy: 6.89 % / Rrim(I) all: 0.109 / Net I/σ(I): 14.34
Reflection shellResolution: 2.465→2.553 Å / Redundancy: 6.42 % / Mean I/σ(I) obs: 2.35 / Num. unique obs: 5173 / % possible all: 96.05

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JUF

5juf


Resolution: 2.465→44.24 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 30.03
RfactorNum. reflection% reflection
Rfree0.2638 5267 5 %
Rwork0.2307 --
obs0.2324 105306 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.465→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9965 0 0 89 10054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210139
X-RAY DIFFRACTIONf_angle_d1.25813643
X-RAY DIFFRACTIONf_dihedral_angle_d13.4753921
X-RAY DIFFRACTIONf_chiral_restr0.0621534
X-RAY DIFFRACTIONf_plane_restr0.0071718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4645-2.49250.40251470.33962801X-RAY DIFFRACTION84
2.4925-2.52180.32741760.33033339X-RAY DIFFRACTION100
2.5218-2.55260.34451770.34283362X-RAY DIFFRACTION100
2.5526-2.58490.40811750.31843312X-RAY DIFFRACTION100
2.5849-2.61890.32441790.29823417X-RAY DIFFRACTION100
2.6189-2.65480.33821770.31173354X-RAY DIFFRACTION100
2.6548-2.69270.34921760.28853395X-RAY DIFFRACTION100
2.6927-2.73290.33891760.2833305X-RAY DIFFRACTION100
2.7329-2.77560.31881800.26643340X-RAY DIFFRACTION100
2.7756-2.82110.29841780.26183391X-RAY DIFFRACTION100
2.8211-2.86970.33821730.26083314X-RAY DIFFRACTION100
2.8697-2.92190.3211770.25973392X-RAY DIFFRACTION100
2.9219-2.97810.31791770.26463330X-RAY DIFFRACTION100
2.9781-3.03880.37311750.28173339X-RAY DIFFRACTION100
3.0388-3.10490.27871780.273339X-RAY DIFFRACTION100
3.1049-3.17710.27631770.26963368X-RAY DIFFRACTION100
3.1771-3.25650.3241760.27143356X-RAY DIFFRACTION100
3.2565-3.34460.30431790.25033358X-RAY DIFFRACTION100
3.3446-3.44290.31291740.26253304X-RAY DIFFRACTION100
3.4429-3.5540.29021790.2433398X-RAY DIFFRACTION100
3.554-3.6810.27891730.24643362X-RAY DIFFRACTION100
3.681-3.82830.29821750.22793317X-RAY DIFFRACTION100
3.8283-4.00240.26281750.21913330X-RAY DIFFRACTION100
4.0024-4.21330.24771770.2053363X-RAY DIFFRACTION100
4.2133-4.4770.22051760.18863377X-RAY DIFFRACTION100
4.477-4.82230.20841760.19163336X-RAY DIFFRACTION100
4.8223-5.30690.22561820.20783354X-RAY DIFFRACTION100
5.3069-6.07310.25981750.2233373X-RAY DIFFRACTION100
6.0731-7.64510.21391770.21233364X-RAY DIFFRACTION100
7.6451-44.25130.13681750.14953349X-RAY DIFFRACTION100

+
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