[English] 日本語
Yorodumi
- PDB-2q0o: Crystal structure of an anti-activation complex in bacterial quor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q0o
TitleCrystal structure of an anti-activation complex in bacterial quorum sensing
Components
  • Probable transcriptional activator protein traR
  • Probable transcriptional repressor traM
KeywordsTRANSCRIPTION / helix-turn-helix / two-helix coiled coil
Function / homology
Function and homology information


quorum sensing / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcriptional repressor TraM / Transcriptional repressor TraM superfamily / Prokaryotic Transcriptional repressor TraM / HR1 repeat / Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal ...Transcriptional repressor TraM / Transcriptional repressor TraM superfamily / Prokaryotic Transcriptional repressor TraM / HR1 repeat / Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Beta-Lactamase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-LAE / Probable transcriptional activator protein TraR / Probable transcriptional repressor TraM
Similarity search - Component
Biological speciesRhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, G. / Jeffrey, P.D. / Fuqua, C. / Shi, Y. / Chen, L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for antiactivation in bacterial quorum sensing.
Authors: Chen, G. / Jeffrey, P.D. / Fuqua, C. / Shi, Y. / Chen, L.
History
DepositionMay 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable transcriptional activator protein traR
B: Probable transcriptional activator protein traR
C: Probable transcriptional repressor traM
D: Probable transcriptional repressor traM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5626
Polymers77,0804
Non-polymers4832
Water8,719484
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.900, 62.480, 65.500
Angle α, β, γ (deg.)94.87, 110.45, 99.17
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Probable transcriptional activator protein traR


Mass: 26324.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium sp. (bacteria) / Strain: NGR234 / Gene: traR / Plasmid: pET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P55407
#2: Protein Probable transcriptional repressor traM


Mass: 12215.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium sp. (bacteria) / Strain: NGR234 / Gene: traM / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P55408
#3: Chemical ChemComp-LAE / 3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE / N-(3-OXO-OCTANAL-1-YL)-HOMOSERINE LACTONE


Mass: 241.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 mM DTT, 60 mM HEPES, 120 mM CaCl2, 16.8% PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.127 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 9, 2005
Details: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 55752 / Num. obs: 53940 / % possible obs: 96.7 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 1.96 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 5.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.96 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 1.3 / Num. unique all: 5580 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L3L

1l3l


Resolution: 2→39.85 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1222632.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2694 5 %RANDOM
Rwork0.235 ---
obs0.235 53915 96.6 %-
all-55735 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.8909 Å2 / ksol: 0.336662 e/Å3
Displacement parametersBiso mean: 40 Å2
Baniso -1Baniso -2Baniso -3
1--5.35 Å20.86 Å26.8 Å2
2---3.77 Å2-1.63 Å2
3---9.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5050 0 34 484 5568
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scbond_it2.432
X-RAY DIFFRACTIONc_scangle_it3.592.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.403 462 5.2 %
Rwork0.403 8393 -
obs-8393 95.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3lae.paramlae.top

+
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