[English] 日本語
Yorodumi
- PDB-6jpi: Crystal structure of PA4674 in complex with its operator DNA (28b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jpi
TitleCrystal structure of PA4674 in complex with its operator DNA (28bp) from Pseudomonas aeruginosa
Components
  • (DNA (28-MER)) x 2
  • HTH cro/C1-type domain-containing protein
KeywordsANTITOXIN/DNA / Toxin-antitoxin system / transcription regulator / ANTITOXIN / 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 / lambda repressor-like DNA-binding domains / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / HTH cro/C1-type domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.143 Å
AuthorsLiu, Y. / Gao, Z. / Zhang, H. / Dong, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaU1732113 China
CitationJournal: To Be Published
Title: Crystal structure of PA4674 in complex with its operator DNA (28bp) from Pseudomonas aeruginosa
Authors: Liu, Y. / Gao, Z. / Zhang, H. / Dong, Y.
History
DepositionMar 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
C: HTH cro/C1-type domain-containing protein
D: HTH cro/C1-type domain-containing protein
E: DNA (28-MER)
F: DNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)66,1386
Polymers66,1386
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13040 Å2
ΔGint-113 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.800, 90.700, 91.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 12232.791 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: PA4674
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9HVC1
#2: DNA chain DNA (28-MER)


Mass: 8523.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria)
#3: DNA chain DNA (28-MER)


Mass: 8683.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M MES, 35% 3-methyl-1,5-pentane diol, 0.2M lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 3.14→50 Å / Num. obs: 11506 / % possible obs: 98.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 74 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.12 / Net I/σ(I): 11.2
Reflection shellResolution: 3.14→3.23 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 807 / CC1/2: 0.978 / Rrim(I) all: 0.754 / % possible all: 94.3

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TRB

3trb


Resolution: 3.143→45.35 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 34.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2808 1157 10.12 %
Rwork0.2151 10279 -
obs0.2218 11436 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.98 Å2 / Biso mean: 91.9144 Å2 / Biso min: 50.4 Å2
Refinement stepCycle: final / Resolution: 3.143→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2925 1148 0 0 4073
Num. residues----425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134271
X-RAY DIFFRACTIONf_angle_d1.5076020
X-RAY DIFFRACTIONf_chiral_restr0.083667
X-RAY DIFFRACTIONf_plane_restr0.008588
X-RAY DIFFRACTIONf_dihedral_angle_d28.2161674
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.143-3.28590.42131310.3536117991
3.2859-3.45910.33351400.284122396
3.4591-3.67570.32471450.2695128798
3.6757-3.95940.32551460.23911298100
3.9594-4.35750.30041450.2087129799
4.3575-4.98740.31931470.2197128497
4.9874-6.28090.2921460.21311336100
6.2809-45.350.20221570.1655137597

+
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