[English] 日本語
Yorodumi
- PDB-3g7z: CcdB dimer in complex with two C-terminal CcdA domains -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3g7z
TitleCcdB dimer in complex with two C-terminal CcdA domains
Components
  • Cytotoxic protein ccdB
  • Protein ccdA
KeywordsTOXIN/TOXIN REPRESSOR / ALPHA+BETA / SH3 domain / intrinsically disordered / TOXIN-TOXIN REPRESSOR COMPLEX
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity / toxin sequestering activity / toxin-antitoxin complex / negative regulation of DNA-templated DNA replication / plasmid maintenance / protein-containing complex disassembly / transcription repressor complex / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Post-segregation antitoxin CcdA / Post-segregation antitoxin CcdA / Toxin CcdB / CcdB protein / SH3 type barrels. - #110 / Plasmid maintenance toxin/Cell growth inhibitor / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Antitoxin CcdA / Toxin CcdB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.351 Å
AuthorsDe Jonge, N. / Loris, R. / Garcia-Pino, A. / Buts, L.
CitationJournal: Mol.Cell / Year: 2009
Title: Rejuvenation of CcdB-Poisoned Gyrase by an Intrinsically Disordered Protein Domain.
Authors: De Jonge, N. / Garcia-Pino, A. / Buts, L. / Haesaerts, S. / Charlier, D. / Zangger, K. / Wyns, L. / De Greve, H. / Loris, R.
History
DepositionFeb 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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: Cytotoxic protein ccdB
B: Cytotoxic protein ccdB
C: Protein ccdA
D: Protein ccdA


Theoretical massNumber of molelcules
Total (without water)32,1974
Polymers32,1974
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.248, 38.377, 62.498
Angle α, β, γ (deg.)90.00, 94.68, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cytotoxic protein ccdB / Protein letB / Protein G / LynB


Mass: 11721.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: tac promotor / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM101 / Gene: ccdB, ECOK12F043, G, letB / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): CSH50 / References: UniProt: P62554
#2: Protein/peptide Protein ccdA / Protein letA / Protein H / LynA


Mass: 4376.829 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 37-72) / Source method: obtained synthetically
Details: Fragment of the CcdA protein encoded on F-plasmid. Synthesised via solid phase syntesis.
References: UniProt: P62552
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIN THIS STRUCTURE TWO CCDA'S (CHAIN C AND D) ARE BOUND TO A DIMER OF CCDB (CHAIN A AND B). CCDB ...IN THIS STRUCTURE TWO CCDA'S (CHAIN C AND D) ARE BOUND TO A DIMER OF CCDB (CHAIN A AND B). CCDB DIMER CAN ONLY ACCOMODATE ONE C-TERMINAL PART OF BOTH CCDA'S. HALF OF THE UNIT CELLS HAVE THE C-TERMINAL HALF OF THE C CHAIN BOUND AND HALF OF THE UNIT CELLS HAVE THE C-TERMINAL HALF OF THE D CHAIN BOUND. THIS IS CLEARLY OBSERVED IN THE DENSITY AND IS NOTED AS ALTERNATIVE CONFORMATIONS FOR THE C-TERMINAL PARTS WITH HALF OCCUPANCIES. THE N-TERMINAL PARTS ARE BOTH BOUND AND CLEARLY SEEN IN THE ELECTRON DENSITY.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M LiSO4, 0.1 M Tris, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 31, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.35→32.674 Å / Num. all: 9426 / Num. obs: 9426 / % possible obs: 80.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.142 / Rsym value: 0.142 / Net I/σ(I): 7.7
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.9 / Num. unique all: 744 / Rsym value: 0.297 / % possible all: 64.6

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZOR chains A,B

2zor
PDB Unreleased entry


Resolution: 2.351→32.674 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.37
Isotropic thermal model: restrained individual isotropic B-factors
Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.272 455 4.83 %random
Rwork0.203 8969 --
obs0.206 9424 80.33 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.183 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso max: 82.25 Å2 / Biso mean: 25.893 Å2 / Biso min: 4.73 Å2
Baniso -1Baniso -2Baniso -3
1--2.678 Å20 Å2-3.119 Å2
2---3.445 Å2-0 Å2
3---9.619 Å2
Refinement stepCycle: LAST / Resolution: 2.351→32.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2092 0 0 113 2205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112134
X-RAY DIFFRACTIONf_angle_d1.042888
X-RAY DIFFRACTIONf_chiral_restr0.076320
X-RAY DIFFRACTIONf_plane_restr0.003368
X-RAY DIFFRACTIONf_dihedral_angle_d16.242760
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3511-2.69120.30241180.233246867
2.6912-3.390.3311630.2224307184
3.39-32.67670.22511740.1823343090

+
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