[English] 日本語
Yorodumi
- PDB-7n10: Co-crystal structure of Prx with ComR DNA binding domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n10
TitleCo-crystal structure of Prx with ComR DNA binding domain
Components
  • ComR
  • Prx
KeywordsVIRAL PROTEIN/TRANSCRIPTION / paratox / ComR / Streptococcus / bacteriophage / quorum sensing / natural competence / VIRAL PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


: / Paratox / 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 / Tetratricopeptide repeat domain ...: / Paratox / 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 / Tetratricopeptide repeat domain / Lambda repressor-like, DNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Paratox / Transcriptional regulator
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M3 (bacteria)
Streptococcus mutans serotype c (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRutbeek, N.R. / Prehna, G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04968 Canada
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Molecular mechanism of quorum sensing inhibition in Streptococcus by the phage protein paratox.
Authors: Rutbeek, N.R. / Rezasoltani, H. / Patel, T.R. / Khajehpour, M. / Prehna, G.
History
DepositionMay 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 8, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: 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: Prx
B: ComR
C: Prx


Theoretical massNumber of molelcules
Total (without water)23,7693
Polymers23,7693
Non-polymers00
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint5 kcal/mol
Surface area7830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.556, 41.918, 90.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Prx


Mass: 8095.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Cloning artifact
Source: (gene. exp.) Streptococcus pyogenes serotype M3 (strain ATCC BAA-595 / MGAS315) (bacteria)
Strain: ATCC BAA-595 / MGAS315 / Gene: SpyM3_1300 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2UWN8
#2: Protein ComR / Putative transcriptional regulator


Mass: 7578.767 Da / Num. of mol.: 1 / Fragment: DNA binding domain (UNP residues 1-66)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans serotype c (strain ATCC 700610 / UA159) (bacteria)
Strain: ATCC 700610 / UA159 / Gene: SMU_61 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DWI6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 1.53 Å3/Da / Density % sol: 19.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 15 mg/mL protein, 20% PEG3500, 0.2 M potassium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.28329 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28329 Å / Relative weight: 1
ReflectionResolution: 1.65→45 Å / Num. obs: 18234 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 24.69 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.027 / Net I/σ(I): 15.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 918 / CC1/2: 0.867 / Rpim(I) all: 0.316 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
Cootmodel building
PHENIXphasing
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CKA

6cka


Resolution: 1.65→45 Å / SU ML: 0.2101 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.9961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1971 1819 5.38 %
Rwork0.175 31977 -
obs0.1763 18234 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.74 Å2
Refinement stepCycle: LAST / Resolution: 1.65→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1051 0 0 188 1239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00421077
X-RAY DIFFRACTIONf_angle_d0.65521448
X-RAY DIFFRACTIONf_chiral_restr0.0461169
X-RAY DIFFRACTIONf_plane_restr0.0079182
X-RAY DIFFRACTIONf_dihedral_angle_d4.9092144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.38161120.35262517X-RAY DIFFRACTION99.81
1.69-1.740.31381630.2922476X-RAY DIFFRACTION99.77
1.74-1.80.25291320.22622419X-RAY DIFFRACTION99.65
1.8-1.870.22241490.21772441X-RAY DIFFRACTION99.62
1.87-1.940.2411210.21242481X-RAY DIFFRACTION98.9
1.94-2.030.23651390.21392473X-RAY DIFFRACTION99.92
2.03-2.130.2191980.17532488X-RAY DIFFRACTION99.65
2.14-2.270.23571260.16912476X-RAY DIFFRACTION99.46
2.27-2.440.19851410.16542439X-RAY DIFFRACTION99.54
2.44-2.690.19371880.16962413X-RAY DIFFRACTION99.85
2.69-3.080.1941470.16352444X-RAY DIFFRACTION99.69
3.08-3.880.17841500.15732464X-RAY DIFFRACTION99.51
3.88-450.15891530.15492446X-RAY DIFFRACTION99.73
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4830779865040.0705588714426-0.2226922565460.432965438456-0.2622152081510.232358202025-0.1298189383780.23415949559-0.186675043665-0.03388089259750.0957477441964-0.04507607012320.1481120297120.3454674095465.04458142586E-50.2845893759920.03851283673370.01104942122720.208065737585-0.0014136660940.24143099470114.4135474732-2.0213814769541.8703309899
20.991050617018-0.0712502272113-0.1747276055370.854657124971-0.3814345361650.622475991615-0.155541441134-0.0158034787944-0.07722377100080.04594239950760.2030983172790.114024895886-0.0870839914561-0.158386737980.005276294569140.1778777560120.004961781207970.005409862304460.1795628340430.02358894211960.1883965083878.695376804326.6638384514638.5858447212
30.749955653676-0.789052632753-0.2544495556761.016571957180.6230894166850.740726596803-0.1214982452840.0882208277212-0.09903440902440.2024584728580.1404121476630.164056154377-0.068994536987-0.1798438678811.17784586346E-50.191633990676-0.001380054009050.03064985491170.1925555840390.04178815773240.2455175050944.340493058124.2551832916139.1850190666
40.554753211506-0.206323366543-0.85057920021.207506088050.7534055781151.573650599570.0593009647549-0.04400610343760.00514867057241-0.01146482950570.0449609747749-0.2161975651970.07223810818810.0230265058979-0.000185676957480.2038959632860.0212511658513-0.005270632363910.251100493851-0.02053614140580.23894472814524.92793463164.0327624366126.9460751733
50.558828795323-0.323083354392-0.8103975252180.3331579536730.5780252041951.40728836695-0.0911202942927-0.0304824082368-0.0269021829939-0.01088556591640.0342971155654-0.07542170594230.1018766286790.0496986580881-6.3534225545E-60.2143656825240.01402301394680.009989084308720.215064161692-0.02129826023160.19542904349822.5800710685-0.30795564108329.1633909476
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 1:16)AA1 - 161 - 16
22(chain A and resid 17:39)AA17 - 3917 - 39
33(chain A and resid 40:60)AA40 - 6040 - 60
44(chain B and resid 1:30)BB1 - 301 - 30
55(chain B and resid 31:66)BB31 - 6631 - 66

+
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