[English] 日本語
Yorodumi
- PDB-7csv: Pseudomonas aeruginosa antitoxin HigA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7csv
TitlePseudomonas aeruginosa antitoxin HigA
ComponentsHTH cro/C1-type domain-containing protein
KeywordsANTITOXIN / dimer
Function / homologyToxin-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 / DNA binding / HTH cro/C1-type domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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

-
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


Theoretical massNumber of molelcules
Total (without water)22,5202
Polymers22,5202
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-22 kcal/mol
Surface area10530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.689, 65.689, 140.392
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11B-218-

HOH

21B-262-

HOH

-
Components

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


Mass: 11259.780 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1.94 Å3/Da / Density % sol: 36.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgCl2, 0.1M Tris pH 8.5, 20% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.707→19.54 Å / Num. obs: 33999 / % possible obs: 99.9 % / Redundancy: 33.8 % / Biso Wilson estimate: 15.87 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.116 / Net I/σ(I): 6.4
Reflection shellResolution: 1.707→1.768 Å / Num. unique obs: 1875 / CC1/2: 0.993

-
Processing

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

6f8h


Resolution: 1.71→19.54 Å / SU ML: 0.195 / Cross valid method: FREE R-VALUE / σ(F): 1.68 / Phase error: 22.5474 / Stereochemistry target values: GeoStd + Monomer Library
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2226 3363 9.89 %
Rwork0.1789 30636 -
obs0.1833 33999 92.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.98 Å2
Refinement stepCycle: LAST / Resolution: 1.71→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 0 135 1667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631563
X-RAY DIFFRACTIONf_angle_d0.80852116
X-RAY DIFFRACTIONf_chiral_restr0.0638232
X-RAY DIFFRACTIONf_plane_restr0.0054280
X-RAY DIFFRACTIONf_dihedral_angle_d15.6284952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.730.29641490.28741367X-RAY DIFFRACTION97.12
1.73-1.760.25021470.22091320X-RAY DIFFRACTION97.35
1.76-1.780.25391510.22851322X-RAY DIFFRACTION96.15
1.78-1.810.31481420.2261355X-RAY DIFFRACTION96.64
1.81-1.850.27071410.20821342X-RAY DIFFRACTION95.68
1.85-1.880.32151360.19841313X-RAY DIFFRACTION96.73
1.88-1.920.26131350.1971322X-RAY DIFFRACTION95.42
1.92-1.950.28021550.18521316X-RAY DIFFRACTION95.21
1.95-20.25081410.18231329X-RAY DIFFRACTION95.39
2-2.040.22311390.18481308X-RAY DIFFRACTION94.89
2.04-2.090.21971420.18831283X-RAY DIFFRACTION93.87
2.09-2.150.20191470.17121308X-RAY DIFFRACTION93.75
2.15-2.210.20711490.16621289X-RAY DIFFRACTION93.56
2.21-2.290.23951410.17431261X-RAY DIFFRACTION92.6
2.29-2.370.18271400.181269X-RAY DIFFRACTION91.91
2.37-2.460.26551390.17561292X-RAY DIFFRACTION92.56
2.46-2.570.22791470.17371253X-RAY DIFFRACTION91.38
2.57-2.710.22751420.18921231X-RAY DIFFRACTION90.27
2.71-2.880.24031340.1881248X-RAY DIFFRACTION90.21
2.88-3.10.23691370.181245X-RAY DIFFRACTION89.62
3.1-3.410.21671260.17311230X-RAY DIFFRACTION88.45
3.41-3.90.17951410.15741194X-RAY DIFFRACTION87.6
3.9-4.90.17421310.14641180X-RAY DIFFRACTION85.41
4.9-19.540.19961110.17351059X-RAY DIFFRACTION75.83

+
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