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- PDB-3vub: CCDB, A TOPOISOMERASE POISON FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 3vub
TitleCCDB, A TOPOISOMERASE POISON FROM E. COLI
ComponentsCCDBChristian Commission for Development in Bangladesh
KeywordsCCDB / TOPOISOMERASE POISON
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity / negative regulation of DNA-templated DNA replication / toxin-antitoxin complex / plasmid maintenance / transcription repressor complex / negative regulation of DNA-templated transcription
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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.4 Å
AuthorsLoris, R. / Dao-Thi, M.-H. / Bahasi, E.M. / Van Melderen, L. / Poortmans, F. / Liddington, R. / Couturier, M. / Wyns, L.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of CcdB, a topoisomerase poison from E. coli.
Authors: Loris, R. / Dao-Thi, M.-H. / Bahassi, E.M. / Van Melderen, L. / Poortmans, F. / Liddington, R. / Couturier, M. / Wyns, L.
History
DepositionApr 17, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CCDB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7572
Polymers11,7221
Non-polymers351
Water2,396133
1
A: CCDB
hetero molecules

A: CCDB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5144
Polymers23,4432
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2250 Å2
ΔGint-35 kcal/mol
Surface area11000 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.870, 36.890, 36.230
Angle α, β, γ (deg.)90.00, 115.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-346-

HOH

21A-347-

HOH

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Components

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


Mass: 11721.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MS501 / Gene: CCDB / Plasmid: PULB2250 / Gene (production host): CCDB / Production host: Escherichia coli (E. coli) / Strain (production host): MS501 / References: UniProt: P62554
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.14 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.6-5.0 mg/mlprotein1drop
26-12 %PEG60001reservoir
310-20 %mPEG50001reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR590 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Sep 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→35 Å / Num. obs: 16670 / % possible obs: 93.5 % / Redundancy: 3.4 % / Rsym value: 0.079 / Net I/σ(I): 22.18
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 5.18 / Rsym value: 0.388 / % possible all: 83.1
Reflection
*PLUS
Num. measured all: 57148 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 83.1 % / Rmerge(I) obs: 0.388

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
MADNESdata reduction
CCP4data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR
Starting model: PRELIMINARY MIR MODEL IN DIFFERENT CRYSTAL FORM

Resolution: 1.4→35 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1321 8 %RANDOM
Rwork0.188 ---
obs0.188 14825 93 %-
Refinement stepCycle: LAST / Resolution: 1.4→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms821 0 1 133 955
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.231
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.95
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.099
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.4→1.46 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.292 152 8 %
Rwork0.29 1754 -
obs--83.1 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.95
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.099

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