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- PDB-2vub: CCDB, A TOPOISOMERASE POISON FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 2vub
TitleCCDB, A TOPOISOMERASE POISON FROM E. COLI
ComponentsCCDBChristian Commission for Development in Bangladesh
KeywordsCCDB / TOPOISOMERASE POISON / PLASMID
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 / MOLECULAR REPLACEMENT / Resolution: 2.45 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 21, 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: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 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
B: CCDB
C: CCDB
D: CCDB
E: CCDB
F: CCDB
G: CCDB
H: CCDB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,94913
Polymers93,7728
Non-polymers1775
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16670 Å2
ΔGint-111 kcal/mol
Surface area32670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.710, 92.980, 142.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.864434, 0.501085, -0.040827), (0.497325, 0.840397, -0.215407), (-0.073626, -0.20651, -0.97567)86.8521, -16.7864, 60.5488
2given(-0.900556, -0.340919, 0.269767), (-0.346424, 0.187835, -0.91908), (0.26266, -0.921137, -0.287258)124.9788, 82.9718, 60.3947
3given(0.598196, -0.789854, -0.135249), (0.456131, 0.196843, 0.867869), (-0.658867, -0.580847, 0.478028)67.4811, -7.225, 80.4532
4given(0.628054, 0.409961, -0.661423), (-0.769514, 0.200769, -0.606251), (-0.115746, 0.889732, 0.441565)17.0302, 99.9124, -25.6341
5given(-0.304897, 0.787715, 0.535297), (0.775286, -0.121157, 0.619881), (0.553144, 0.604008, -0.573764)26.2236, -3.1145, -27.8712
6given(-0.297666, -0.233968, 0.925556), (-0.233848, -0.922099, -0.308301), (0.925586, -0.30821, 0.219765)68.6403, 118.1529, -22.2604
7given(0.13231, -0.568884, -0.811705), (-0.254176, -0.810995, 0.526955), (-0.958065, 0.136595, -0.251899)99.904, 94.2341, 78.3191

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Components

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


Mass: 11721.508 Da / Num. of mol.: 8
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.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growpH: 9 / Details: pH 9.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 9 / PH range high: 6.5
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1ammonium sulfate1reservoir
2sodium chloride1reservoir
3sodium acetate1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→15 Å / Num. obs: 36967 / % possible obs: 96.3 % / Redundancy: 4.86 % / Rsym value: 0.093 / Net I/σ(I): 14.39
Reflection shellResolution: 2.45→2.56 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.76 / Rsym value: 0.422 / % possible all: 92.2
Reflection
*PLUS
Num. measured all: 179543 / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
% possible obs: 92.2 % / Rmerge(I) obs: 0.422

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TETRAGONAL CRYSTAL FORM OF CCDB

Resolution: 2.45→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2226 6 %RANDOM
Rwork0.205 ---
obs0.205 36967 96.3 %-
Refinement stepCycle: LAST / Resolution: 2.45→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3685 0 5 195 3885
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.342
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.242
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
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.45→2.56 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.36 280 6 %
Rwork0.296 4078 -
obs--92.2 %
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_deg26.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.242

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