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- PDB-3hpw: CcdB dimer in complex with one C-terminal CcdA domain -

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Basic information

Entry
Database: PDB / ID: 3hpw
TitleCcdB dimer in complex with one C-terminal CcdA domain
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
DI(HYDROXYETHYL)ETHER / Antitoxin CcdA / Toxin CcdB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.452 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
DepositionJun 5, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytotoxic protein ccdB
B: Cytotoxic protein ccdB
C: Protein ccdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0225
Polymers27,8203
Non-polymers2022
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-45 kcal/mol
Surface area10850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.357, 38.038, 69.651
Angle α, β, γ (deg.)90.00, 97.51, 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 / Fragment: CcdB
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.: 1 / 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 synthesis by Bio-Synthesis.
References: UniProt: P62552
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O

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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: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 22% PEG4000, 0.1M Tris-HCl pH7.4, 0.2M LiSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 1.45→15.78 Å / Num. all: 36688 / Num. obs: 36600 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 18.3
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 7.8 / Num. unique all: 3705 / Rsym value: 0.107 / % possible all: 98.2

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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: CcdB2 dimer, PDB entry 2VUB, chain A,B

2vub


Resolution: 1.452→15.785 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.892 / SU ML: 0.18 / Isotropic thermal model: anisotropic B factor refinement / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1827 4.99 %random
Rwork0.165 34773 --
obs0.167 36600 95.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.642 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso max: 82.74 Å2 / Biso mean: 15.252 Å2 / Biso min: 4.34 Å2
Baniso -1Baniso -2Baniso -3
1--1.041 Å2-0 Å20.672 Å2
2--0.236 Å2-0 Å2
3---0.805 Å2
Refinement stepCycle: LAST / Resolution: 1.452→15.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1916 0 5 335 2256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081976
X-RAY DIFFRACTIONf_angle_d1.1622690
X-RAY DIFFRACTIONf_chiral_restr0.079299
X-RAY DIFFRACTIONf_plane_restr0.005343
X-RAY DIFFRACTIONf_dihedral_angle_d14.733744
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.452-1.4920.2081240.1662698282297
1.492-1.5360.1971370.1562718285598
1.536-1.5850.1851290.1522765289498
1.585-1.6420.181450.1532686283198
1.642-1.7070.1791450.152701284698
1.707-1.7850.2011330.1552712284597
1.785-1.8790.2231450.1592723286898
1.879-1.9960.2091560.1582652280896
1.996-2.150.1731500.1452668281896
2.15-2.3660.171420.1542640278295
2.366-2.7070.231290.1732671280095
2.707-3.4050.2131560.1712589274593
3.405-15.7860.1951360.1662550268688
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.40080.0163-0.24830.3124-0.07910.4223-0.01490.0115-0.0115-0.01970.0053-0.0865-0.0196-0.0002-0.04250.0292-0.00120.00090.0295-0.0060.0544-2.40313.2294-28.8269
20.23880.0605-0.03380.46720.00480.2932-0.051-0.0584-0.02420.08420.03150.0596-0.081-0.10100.07070.02750.00380.07450.00160.0431-16.95444.4293-11.6656
30.0493-0.1129-0.05860.06980.07590.1411-0.0328-0.0479-0.04990.08470.0195-0.0923-0.02680.0197-0.00020.1370.0118-0.03180.12970.0070.1135-3.3032-0.2904-9.3166
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 101
2X-RAY DIFFRACTION2chain BB1 - 101
3X-RAY DIFFRACTION3chain CC40 - 72

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