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- PDB-3tcj: CcdB dimer from V. fisheri in complex with one C-terminal domain ... -

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Basic information

Entry
Database: PDB / ID: 3tcj
TitleCcdB dimer from V. fisheri in complex with one C-terminal domain of F-plasmid CcdA
Components
  • CcdB
  • Protein CcdA
KeywordsTOXIN/ANTITOXIN / ALPHA+BETA SH3 domain intrinsically disordered / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity / plasmid maintenance / 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
ACETATE ION / Antitoxin CcdA / Toxin CcdB
Similarity search - Component
Biological speciesAliivibrio fischeri (bacteria)
Escherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsDe Jonge, N. / Loris, R.
Citation
Journal: J.Am.Chem.Soc. / Year: 2013
Title: Energetic basis of uncoupling folding from binding for an intrinsically disordered protein.
Authors: Drobnak, I. / De Jonge, N. / Haesaerts, S. / Vesnaver, G. / Loris, R. / Lah, J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Purification and crystallization of Vibrio fischeri CcdB and its complexes with fragments of gyrase and CcdA.
Authors: De Jonge, N. / Buts, L. / Vangelooven, J. / Mine, N. / Van Melderen, L. / Wyns, L. / Loris, R.
History
DepositionAug 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Structure summary
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Sep 13, 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: CcdB
B: CcdB
T: Protein CcdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1954
Polymers28,1363
Non-polymers591
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-40 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.864, 62.561, 81.951
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsHeterodimer consisting of one CcdB dimer to which one CcdA37-72 fragment is bound. The biological unit corresponds to the asymmetric unit

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Components

#1: Protein CcdB


Mass: 11879.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aliivibrio fischeri (bacteria) / Gene: ccdB / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): B462 / References: UniProt: Q84B82
#2: Protein/peptide Protein CcdA / LynA / Protein H / Protein LetA


Mass: 4376.829 Da / Num. of mol.: 1 / Fragment: unp residues 37-72 / Source method: obtained synthetically / Source: (synth.) Escherichia coli O157:H7 (bacteria) / References: UniProt: P62553
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 293 K / pH: 4.6
Details: 8% PEG4000, 0.1M CH3COONa.3H2O, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.808
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.808 Å / Relative weight: 1
ReflectionResolution: 1.9→49.8 Å / Num. obs: 18030 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 20.86 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 15.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 6 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 4.07 / Rsym value: 0.0452 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JRZ

3jrz


Resolution: 1.93→19.47 Å / SU ML: 0.29 / Isotropic thermal model: Anisotropic B factors / σ(F): 1.34 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.252 914 5.08 %
Rwork0.192 --
obs0.195 17993 96.7 %
all-17993 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.99 Å2 / ksol: 0.29 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.2222 Å20 Å20 Å2
2--5.0082 Å2-0 Å2
3----1.786 Å2
Refinement stepCycle: LAST / Resolution: 1.93→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 4 205 2058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021901
X-RAY DIFFRACTIONf_angle_d0.6022593
X-RAY DIFFRACTIONf_dihedral_angle_d15.607681
X-RAY DIFFRACTIONf_chiral_restr0.043311
X-RAY DIFFRACTIONf_plane_restr0.002334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9337-2.03550.27631280.22772187X-RAY DIFFRACTION89
2.0355-2.16290.30261290.20952339X-RAY DIFFRACTION94
2.1629-2.32960.24641400.19572355X-RAY DIFFRACTION95
2.3296-2.56360.26761170.20182468X-RAY DIFFRACTION98
2.5636-2.93350.27031430.20662497X-RAY DIFFRACTION100
2.9335-3.69180.2311360.19112546X-RAY DIFFRACTION100
3.6918-19.47130.22471210.16762687X-RAY DIFFRACTION100
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)
10.2509-0.40190.40340.6475-0.81180.95390.1846-0.14540.02290.2969-0.1707-0.0852-0.17410.0789-00.12740.00450.01750.16490.04640.143444.893555.695221.9782
20.67420.0485-0.85890.5575-0.41151.4962-0.05430.31770.1770.112-0.0138-0.0264-0.026-0.01180.00010.10710.003-0.00370.08660.01920.105139.51553.837326.9955
30.5682-0.28040.53551.3958-1.0220.77870.0340.2987-0.169-0.0032-0.05990.0202-0.08550.1589-0.00010.12060.01690.01060.17230.01820.136745.49551.075329.9684
40.20360.1785-0.01290.57810.0481.0736-0.07640.0782-0.2158-0.0176-0.0865-0.05660.6575-0.3189-0.00070.1809-0.00120.01220.10120.02970.121838.853247.10130.7383
51.31860.36640.48840.84371.21941.1083-0.02530.01160.23930.02170.0683-0.1957-0.1630.24830.00280.1093-0.02220.01510.07190.01640.138834.643866.098941.6767
6-0.0841-0.0702-0.0220.160.11080.12750.23261.184-0.1503-0.8317-0.36260.91290.3152-0.2157-0.00480.25790.0043-0.06930.47410.15590.369617.768665.110332.76
70.6016-0.20820.55381.71040.20351.1862-0.1232-0.02110.0743-0.05530.12230.014-0.1582-0.066100.1398-0.00330.02350.15750.00290.154229.103166.361441.1739
80.42990.2747-0.00180.51210.01790.1667-0.01970.04680.02730.18350.0291-0.02720.3386-0.23890.00010.1202-0.01390.01290.10770.03420.134625.815254.005540.8676
9-0.00810.05170.04380.14970.02470.1785-0.02211.1865-0.92-0.20250.16190.80230.16670.1528-0.0010.2543-0.0626-0.01690.4932-0.09280.317316.011350.135222.5867
100.0841-0.0077-0.02250.0731-0.18950.0420.01710.3371-0.6072-0.71990.37420.1689-0.60360.5716-0.00140.4604-0.1176-0.01430.34840.03910.289219.387461.993323.5829
110.0395-0.01580.01640.0051-0.00650.0202-0.08370.116-0.28860.5156-0.19920.3481-0.2608-0.105500.8952-0.33050.00930.42390.16550.329725.921371.71226.1644
12-0.0030.0816-0.1520.0258-0.00350.04970.4096-0.1485-0.6568-1.51950.0394-1.39480.29011.60560.00040.4848-0.00530.20440.490.01470.531938.920566.810630.4333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:21)
2X-RAY DIFFRACTION2(chain A and resid 22:48)
3X-RAY DIFFRACTION3(chain A and resid 49:79)
4X-RAY DIFFRACTION4(chain A and resid 80:105)
5X-RAY DIFFRACTION5(chain B and resid 2:42)
6X-RAY DIFFRACTION6(chain B and resid 43:53)
7X-RAY DIFFRACTION7(chain B and resid 54:86)
8X-RAY DIFFRACTION8(chain B and resid 87:105)
9X-RAY DIFFRACTION9(chain T and resid 40:47)
10X-RAY DIFFRACTION10(chain T and resid 48:57)
11X-RAY DIFFRACTION11(chain T and resid 58:63)
12X-RAY DIFFRACTION12(chain T and resid 64:72)

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