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- PDB-3g7z: CcdB dimer in complex with two C-terminal CcdA domains -

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Basic information

Entry
Database: PDB / ID: 3g7z
TitleCcdB dimer in complex with two C-terminal CcdA domains
Components
  • Cytotoxic protein ccdBCytotoxicity
  • 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 / negative regulation of DNA-templated DNA replication / protein-containing complex disassembly / toxin-antitoxin complex / plasmid maintenance / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

#1: Protein Cytotoxic protein ccdB / Cytotoxicity / 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 / 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.

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Experimental details

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Experiment

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

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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

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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

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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

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