[English] 日本語
Yorodumi
- PDB-7amn: Structure of LuxR with DNA (repression) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7amn
TitleStructure of LuxR with DNA (repression)
Components
  • DNA (5'-D(P*TP*AP*TP*TP*GP*AP*TP*AP*AP*AP*AP*TP*TP*AP*TP*CP*AP*AP*TP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*AP*TP*TP*GP*AP*TP*AP*AP*TP*TP*TP*TP*AP*TP*CP*AP*AP*TP*A)-3')
  • HTH-type transcriptional regulator LuxR
KeywordsTRANSCRIPTION / transcription factor / DNA
Function / homologyTetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / DNA binding / DNA / DNA (> 10) / LuxR family transcriptional regulator
Function and homology information
Biological speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsLiu, B. / Reverter, D.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-098423-B-I00 Spain
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Binding site profiles and N-terminal minor groove interactions of the master quorum-sensing regulator LuxR enable flexible control of gene activation and repression.
Authors: Zhang, J. / Liu, B. / Gu, D. / Hao, Y. / Chen, M. / Ma, Y. / Zhou, X. / Reverter, D. / Zhang, Y. / Wang, Q.
History
DepositionOct 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: HTH-type transcriptional regulator LuxR
A: HTH-type transcriptional regulator LuxR
E: DNA (5'-D(P*TP*AP*TP*TP*GP*AP*TP*AP*AP*AP*AP*TP*TP*AP*TP*CP*AP*AP*TP*AP*A)-3')
F: DNA (5'-D(P*TP*TP*AP*TP*TP*GP*AP*TP*AP*AP*TP*TP*TP*TP*AP*TP*CP*AP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)63,4874
Polymers63,4874
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9430 Å2
ΔGint-53 kcal/mol
Surface area22460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.339, 69.339, 123.206
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein HTH-type transcriptional regulator LuxR / LuxR family transcriptional regulator / Quorum sensing regulator LuxR / Quorum-sensing II master ...LuxR family transcriptional regulator / Quorum sensing regulator LuxR / Quorum-sensing II master regulator / TetR/AcrR family transcriptional regulator


Mass: 25304.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria)
Gene: valR, luxR, AL539_16930, AOG25_16695, AT730_08150, K06K5_26160
Production host: Escherichia coli (E. coli) / References: UniProt: B4X9Q4
#2: DNA chain DNA (5'-D(P*TP*AP*TP*TP*GP*AP*TP*AP*AP*AP*AP*TP*TP*AP*TP*CP*AP*AP*TP*AP*A)-3')


Mass: 6452.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio alginolyticus (bacteria)
#3: DNA chain DNA (5'-D(P*TP*TP*AP*TP*TP*GP*AP*TP*AP*AP*TP*TP*TP*TP*AP*TP*CP*AP*AP*TP*A)-3')


Mass: 6425.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio alginolyticus (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 50mM Sodium Formate, 50mM Tris PH7.5, 22% PEG 2000MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 8, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.236→61.603 Å / Num. obs: 28010 / % possible obs: 99.7 % / Redundancy: 5 % / CC1/2: 0.99 / Net I/σ(I): 15.3
Reflection shellResolution: 2.236→2.244 Å / Num. unique obs: 280 / CC1/2: 0.46

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→49.03 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2424 1259 4.89 %
Rwork0.2099 24464 -
obs0.2115 25723 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 206.71 Å2 / Biso mean: 83.57 Å2 / Biso min: 35.49 Å2
Refinement stepCycle: final / Resolution: 2.3→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3044 861 0 23 3928
Biso mean---80.09 -
Num. residues----417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054069
X-RAY DIFFRACTIONf_angle_d0.8225686
X-RAY DIFFRACTIONf_chiral_restr0.033643
X-RAY DIFFRACTIONf_plane_restr0.003584
X-RAY DIFFRACTIONf_dihedral_angle_d21.5181536
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.39210.3421280.30272751100
2.3921-2.5010.31171550.27842676100
2.501-2.63280.30041320.26432728100
2.6328-2.79780.33251480.27842714100
2.7978-3.01380.29021370.26742736100
3.0138-3.3170.27431090.2416270298
3.317-3.79680.24511790.2104267599
3.7968-4.7830.23441400.19142717100
4.783-49.030.19321310.1709276599
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)
15.91291.7752-0.08186.39460.35822.6737-0.29990.60520.7688-0.55030.24151.1857-0.3434-0.66930.05520.6640.0989-0.10390.55270.04810.5724-9.16924.3673-4.4487
25.1277-0.60531.52294.0833-0.75033.4408-0.22270.0283-0.2525-0.15260.29360.52780.03-0.851-0.05120.5049-0.07690.04680.5476-0.05580.3676-9.91451.1028-3.0093
32.006-0.17870.7079.4839-0.9011.99320.0779-0.0934-0.10750.9917-0.4651-2.4377-0.11750.19840.3120.5684-0.062-0.16620.4314-0.06361.230521.469911.54318.2877
42.19251.63650.63592.1442-0.85871.46030.1993-0.0715-0.03620.1534-0.6802-2.3758-0.24780.14860.41070.74890.0403-0.1540.4401-0.00221.117121.439710.60288.4096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq -10:9999)A-10 - 9999
2X-RAY DIFFRACTION2(chain B and resseq -10:9999)B-10 - 9999
3X-RAY DIFFRACTION3(chain E and resseq -10:9999)E-10 - 9999
4X-RAY DIFFRACTION4(chain F and resseq -10:9999)F-10 - 9999

+
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