[English] 日本語
Yorodumi
- PDB-7csy: Pseudomonas aeruginosa antitoxin HigA with higBA promoter -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7csy
TitlePseudomonas aeruginosa antitoxin HigA with higBA promoter
Components
  • DNA (28-MER)
  • DNA (29-MER)
  • HTH cro/C1-type domain-containing protein
KeywordsANTITOXIN/DNA / dimer / ANTITOXIN-DNA COMPLEX
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Toxin-antitoxin system, antidote protein, HigA / Helix-turn-helix / 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
THYMIDINE-5'-PHOSPHATE / DNA / DNA (> 10) / HTH cro/C1-type domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsSong, Y.J. / Luo, G.H. / Bao, R.
CitationJournal: Environ.Microbiol. / Year: 2021
Title: Pseudomonas aeruginosa antitoxin HigA functions as a diverse regulatory factor by recognizing specific pseudopalindromic DNA motifs.
Authors: Song, Y. / Luo, G. / Zhu, Y. / Li, T. / Li, C. / He, L. / Zhao, N. / Zhao, C. / Yang, J. / Huang, Q. / Mu, X. / Tang, X. / Kang, M. / Wu, S. / He, Y. / Bao, R.
History
DepositionAug 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HTH cro/C1-type domain-containing protein
B: HTH cro/C1-type domain-containing protein
C: HTH cro/C1-type domain-containing protein
D: HTH cro/C1-type domain-containing protein
E: DNA (28-MER)
F: DNA (29-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8577
Polymers62,5346
Non-polymers3221
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13010 Å2
ΔGint-115 kcal/mol
Surface area26360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.255, 100.433, 68.795
Angle α, β, γ (deg.)90.000, 114.214, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein
HTH cro/C1-type domain-containing protein


Mass: 11259.780 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA4674 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HVC1
#2: DNA chain DNA (28-MER)


Mass: 8667.626 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: DNA chain DNA (29-MER)


Mass: 8827.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#4: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.36 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 35% (v/v) 2-methyl-2,4-pentanediol, 0.1M HEPES pH7.5, 0.1M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.29→29.66 Å / Num. obs: 71719 / % possible obs: 98.78 % / Redundancy: 5.6 % / Biso Wilson estimate: 43.15 Å2 / CC1/2: 0.596 / Net I/σ(I): 33.8
Reflection shellResolution: 2.29→2.368 Å / Num. unique obs: 3415 / CC1/2: 0.401

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F8H

6f8h


Resolution: 2.29→29.66 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 29.7627 / Stereochemistry target values: GeoStd + Monomer Library
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2467 3870 5.4 %
Rwork0.2092 67849 -
obs0.2113 71719 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.44 Å2
Refinement stepCycle: LAST / Resolution: 2.29→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 1167 20 57 4216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00864360
X-RAY DIFFRACTIONf_angle_d1.05456145
X-RAY DIFFRACTIONf_chiral_restr0.0541681
X-RAY DIFFRACTIONf_plane_restr0.0071600
X-RAY DIFFRACTIONf_dihedral_angle_d19.04112424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.310.39421070.36081871X-RAY DIFFRACTION75.5
2.31-2.340.33981340.34452428X-RAY DIFFRACTION96.39
2.34-2.370.36481380.3062401X-RAY DIFFRACTION97.13
2.37-2.410.33111410.30462393X-RAY DIFFRACTION96.9
2.41-2.440.34771370.31182399X-RAY DIFFRACTION95.99
2.44-2.480.40251410.31552409X-RAY DIFFRACTION97.44
2.48-2.520.33831360.30232380X-RAY DIFFRACTION96.81
2.52-2.560.34971400.28142435X-RAY DIFFRACTION98.13
2.56-2.60.31861410.27162466X-RAY DIFFRACTION97.68
2.6-2.650.30991400.26712456X-RAY DIFFRACTION97.63
2.65-2.70.28571400.2592444X-RAY DIFFRACTION97.92
2.7-2.750.35931360.26832376X-RAY DIFFRACTION97.9
2.75-2.810.35711370.26212427X-RAY DIFFRACTION98.24
2.81-2.880.30471370.25542513X-RAY DIFFRACTION98.26
2.88-2.950.30931400.25522424X-RAY DIFFRACTION99
2.95-3.030.30711380.26052448X-RAY DIFFRACTION98.89
3.03-3.120.35751400.26352483X-RAY DIFFRACTION98.35
3.12-3.220.25051350.23092423X-RAY DIFFRACTION98.12
3.22-3.340.26441390.20242465X-RAY DIFFRACTION99.24
3.34-3.470.20231400.19222456X-RAY DIFFRACTION98.41
3.47-3.630.23171430.2052463X-RAY DIFFRACTION99.05
3.63-3.820.24341440.19792452X-RAY DIFFRACTION99.58
3.82-4.060.20451410.17612490X-RAY DIFFRACTION99.62
4.06-4.370.19071410.16082480X-RAY DIFFRACTION99.47
4.37-4.810.17961400.15862465X-RAY DIFFRACTION99.73
4.81-5.50.20541430.17172473X-RAY DIFFRACTION99.66
5.5-6.910.22751430.17422490X-RAY DIFFRACTION99.62
6.91-29.660.1651380.15192439X-RAY DIFFRACTION98.25

+
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