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- PDB-3jrz: CcdBVfi-FormII-pH5.6 -

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Basic information

Entry
Database: PDB / ID: 3jrz
TitleCcdBVfi-FormII-pH5.6
ComponentsCcdBChristian Commission for Development in Bangladesh
KeywordsTOXIN / ALPHA+BETA / SH3 domain
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity / plasmid maintenance
Similarity search - Function
Toxin CcdB / CcdB protein / SH3 type barrels. - #110 / Plasmid maintenance toxin/Cell growth inhibitor / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesVibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDe Jonge, N. / Buts, L. / Loris, R.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Structural and thermodynamic characterization of vibrio fischeri CCDB
Authors: De Jonge, N. / Hohlweg, W. / Garcia-Pino, A. / Respondek, M. / Buts, L. / Haesaerts, S. / Lah, J. / Zangger, K. / Loris, R.
#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
DepositionSep 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CcdB


Theoretical massNumber of molelcules
Total (without water)11,8801
Polymers11,8801
Non-polymers00
Water1,31573
1
A: CcdB

A: CcdB


Theoretical massNumber of molelcules
Total (without water)23,7592
Polymers23,7592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1870 Å2
ΔGint-17 kcal/mol
Surface area9800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.506, 43.624, 37.489
Angle α, β, γ (deg.)90.00, 110.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CcdB / Christian Commission for Development in Bangladesh


Mass: 11879.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: tac promotor / Source: (gene. exp.) Vibrio fischeri (bacteria) / Gene: ccdB / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): B462 / References: UniProt: Q84B82
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.89 Å3/Da / Density % sol: 34.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100mM sodium citrate pH5.6, 2% polyethyleneimine, 500mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8162 Å
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: 0.8162 Å / Relative weight: 1
ReflectionResolution: 1.7→19.9 Å / Num. all: 9956 / Num. obs: 9956 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.31 % / Biso Wilson estimate: 17.46 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 22.98
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 8 / Num. unique all: 986 / Rsym value: 0.237 / % 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: PDB ENTRY 3JSC

3jsc


Resolution: 1.7→18.776 Å / Occupancy max: 1 / Occupancy min: 0.49 / FOM work R set: 0.879 / SU ML: 0.22 / Isotropic thermal model: individual atomic B factors / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 0 / Phase error: 18.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1989 475 4.82 %random
Rwork0.1676 9387 --
obs0.1692 9862 99.92 %-
all-9862 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.977 Å2 / ksol: 0.414 e/Å3
Displacement parametersBiso max: 45.63 Å2 / Biso mean: 18.774 Å2 / Biso min: 9.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.044 Å20 Å20.188 Å2
2--0.07 Å2-0 Å2
3----0.114 Å2
Refinement stepCycle: LAST / Resolution: 1.7→18.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms775 0 0 73 848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011785
X-RAY DIFFRACTIONf_angle_d1.3951074
X-RAY DIFFRACTIONf_chiral_restr0.115136
X-RAY DIFFRACTIONf_plane_restr0.008136
X-RAY DIFFRACTIONf_dihedral_angle_d17.952283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.94590.2031610.16553108X-RAY DIFFRACTION100
1.9459-2.45070.19641590.14293121X-RAY DIFFRACTION100
2.4507-18.77750.19731550.17833158X-RAY DIFFRACTION100

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