[English] 日本語
Yorodumi
- PDB-8sva: Structure of the Rhodococcus sp. USK13 DarR-20 bp DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sva
TitleStructure of the Rhodococcus sp. USK13 DarR-20 bp DNA complex
Components
  • DNA (5'-D(*TP*AP*GP*AP*TP*AP*CP*TP*CP*CP*GP*GP*AP*GP*TP*AP*TP*CP*TP*A)-3')
  • TetR/AcrR family transcriptional regulator
KeywordsTRANSCRIPTION/DNA / transcription / repressor / DarR / M. smegmatis / TetR / TFR / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


HTH-type transcriptional repressor KstR2, C-terminal / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracyclin 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
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / TetR/AcrR family transcriptional regulator
Similarity search - Component
Biological speciesRhodococcus sp. USK13 (bacteria)
Rhodococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.96 Å
AuthorsSchumacher, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM130290 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structures of the DarR transcription regulator reveal unique modes of second messenger and DNA binding.
Authors: Schumacher, M.A. / Lent, N. / Chen, V.B. / Salinas, R.
History
DepositionMay 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Feb 28, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TetR/AcrR family transcriptional regulator
F: TetR/AcrR family transcriptional regulator
G: TetR/AcrR family transcriptional regulator
T: TetR/AcrR family transcriptional regulator
B: DNA (5'-D(*TP*AP*GP*AP*TP*AP*CP*TP*CP*CP*GP*GP*AP*GP*TP*AP*TP*CP*TP*A)-3')
D: DNA (5'-D(*TP*AP*GP*AP*TP*AP*CP*TP*CP*CP*GP*GP*AP*GP*TP*AP*TP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,3527
Polymers107,2576
Non-polymers951
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-97 kcal/mol
Surface area39590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.894, 128.894, 113.929
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein
TetR/AcrR family transcriptional regulator


Mass: 23747.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: 100% match to NCBI Reference Sequence: WP_213575646.1
Source: (gene. exp.) Rhodococcus sp. USK13 (bacteria) / Gene: C5613_22450 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S8J6Y8
#2: DNA chain DNA (5'-D(*TP*AP*GP*AP*TP*AP*CP*TP*CP*CP*GP*GP*AP*GP*TP*AP*TP*CP*TP*A)-3')


Mass: 6132.991 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Rhodococcus (bacteria)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsEntity 1 TetR/AcrR family transcriptional regulator is a 100% match to NCBI Reference Sequence: WP_213575646.1

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.5, 30% PEG 8000 and 0.1 M Calcium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.989 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 2.96→42.19 Å / Num. obs: 22523 / % possible obs: 99.7 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rpim(I) all: 0.064 / Rsym value: 0.163 / Net I/σ(I): 8.9
Reflection shellResolution: 2.96→3.03 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1477 / CC1/2: 0.137 / Rpim(I) all: 1.575

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALAdata scaling
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.96→42.19 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2761 2007 8.97 %
Rwork0.2392 --
obs0.2424 22369 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.96→42.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6072 732 5 24 6833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013
X-RAY DIFFRACTIONf_angle_d0.936
X-RAY DIFFRACTIONf_dihedral_angle_d22.2892572
X-RAY DIFFRACTIONf_chiral_restr0.0511098
X-RAY DIFFRACTIONf_plane_restr0.0061135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.96-3.030.51641240.46581317X-RAY DIFFRACTION90
3.03-3.110.42791440.4291431X-RAY DIFFRACTION99
3.11-3.20.35171470.3561480X-RAY DIFFRACTION100
3.2-3.310.35381450.32371477X-RAY DIFFRACTION100
3.31-3.420.30681440.3031451X-RAY DIFFRACTION100
3.42-3.560.35161480.29761447X-RAY DIFFRACTION100
3.56-3.720.32871450.25991466X-RAY DIFFRACTION100
3.72-3.920.28651450.23791477X-RAY DIFFRACTION100
3.92-4.160.28241450.2221453X-RAY DIFFRACTION100
4.16-4.490.2421440.21231462X-RAY DIFFRACTION100
4.49-4.930.25511470.20941473X-RAY DIFFRACTION100
4.94-5.650.281380.22881457X-RAY DIFFRACTION100
5.65-7.110.29061430.24771482X-RAY DIFFRACTION99
7.11-42.190.19611480.17311489X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -47.5104 Å / Origin y: -5.2229 Å / Origin z: 0.7496 Å
111213212223313233
T0.4134 Å20.0126 Å20.0208 Å2-0.5046 Å2-0.053 Å2--0.7054 Å2
L0.5603 °2-0.4056 °20.0025 °2-0.6223 °2-0.0589 °2--2.702 °2
S-0.1239 Å °-0.2085 Å °-0.0029 Å °0.0867 Å °0.0842 Å °0.145 Å °-0.026 Å °-0.3006 Å °0.0222 Å °
Refinement TLS groupSelection details: all

+
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