[English] 日本語
Yorodumi
- PDB-7t5u: Structure of E. coli MS115-1 CapH N-terminal domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7t5u
TitleStructure of E. coli MS115-1 CapH N-terminal domain
ComponentsHelix-turn-helix domain-containing protein
KeywordsDNA BINDING PROTEIN / Helix turn helix / HTH / DdrO
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
Helix-turn-helix domain / : / 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
Similarity search - Domain/homology
Helix-turn-helix domain-containing protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsLau, R.K. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI148814 United States
CitationJournal: Embo J. / Year: 2022
Title: A conserved signaling pathway activates bacterial CBASS immune signaling in response to DNA damage.
Authors: Lau, R.K. / Enustun, E. / Gu, Y. / Nguyen, J.V. / Corbett, K.D.
History
DepositionDec 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Apr 3, 2024Group: 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: Helix-turn-helix domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8713
Polymers7,6791
Non-polymers1922
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.374, 39.715, 47.231
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 Helix-turn-helix domain-containing protein / Helix-turn-helix transcriptional regulator / Transcriptional regulator / XRE family transcriptional regulator


Mass: 7678.672 Da / Num. of mol.: 1 / Fragment: HTH cro/C1-type domain, residues 2-67
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: nadR_1, BHS87_27750, D9K17_19515, GRQ19_13110, HV109_14215, NCTC13216_00230
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X1LKI5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M acetate pH 4.5, 2 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.02→39.72 Å / Num. obs: 25495 / % possible obs: 80.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 8.99 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.03 / Net I/σ(I): 12.5
Reflection shellResolution: 1.02→1.04 Å / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2 / Num. unique obs: 136 / CC1/2: 0.754 / Rpim(I) all: 0.298 / % possible all: 8.7

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ideal alpha helix

Resolution: 1.02→30.4 Å / SU ML: 0.0825 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.4139
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1764 1197 4.7 %
Rwork0.163 24251 -
obs0.1637 25448 80.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.21 Å2
Refinement stepCycle: LAST / Resolution: 1.02→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms517 0 10 87 614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083547
X-RAY DIFFRACTIONf_angle_d0.9929738
X-RAY DIFFRACTIONf_chiral_restr0.06981
X-RAY DIFFRACTIONf_plane_restr0.009294
X-RAY DIFFRACTIONf_dihedral_angle_d13.8966211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.02-1.060.17140.1777507X-RAY DIFFRACTION15.13
1.06-1.110.1555680.15221420X-RAY DIFFRACTION43.13
1.11-1.170.13021090.13352427X-RAY DIFFRACTION73.15
1.17-1.240.17841540.12843195X-RAY DIFFRACTION96.21
1.24-1.340.13311560.12893244X-RAY DIFFRACTION98.41
1.34-1.470.18091680.13123273X-RAY DIFFRACTION98.48
1.47-1.690.15741680.13613299X-RAY DIFFRACTION98.94
1.69-2.120.16731640.16283383X-RAY DIFFRACTION99.89
2.13-30.40.19541960.19113503X-RAY DIFFRACTION99.97

+
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