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- PDB-1vub: CCDB, A TOPOISOMERASE POISON FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1vub
TitleCCDB, A TOPOISOMERASE POISON FROM E. COLI
ComponentsCCDB
KeywordsPLASMID / CCDB / TOPOISOMERASE POISON / PLASMID ADDICTION
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity / toxin-antitoxin complex / negative regulation of DNA-templated DNA replication / 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: 2.6 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 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0288
Polymers46,8864
Non-polymers1424
Water66737
1
A: CCDB
B: CCDB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5144
Polymers23,4432
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-36 kcal/mol
Surface area10020 Å2
MethodPISA
2
C: CCDB
D: CCDB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5144
Polymers23,4432
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-37 kcal/mol
Surface area10180 Å2
MethodPISA
3
A: CCDB
B: CCDB
hetero molecules

A: CCDB
B: CCDB
hetero molecules

C: CCDB
D: CCDB
hetero molecules

C: CCDB
D: CCDB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,05616
Polymers93,7728
Non-polymers2848
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation4_564y+1/2,-x+3/2,z-1/21
crystal symmetry operation5_655-x+3/2,y+1/2,-z+1/21
Buried area17690 Å2
ΔGint-186 kcal/mol
Surface area31910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.520, 104.520, 88.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.995817, 0.090338, -0.013681), (0.090457, -0.995865, 0.008378), (-0.012868, -0.00958, -0.999871)-6.53812, 144.88853, 1.55263
2given(0.996645, 0.081556, 0.006934), (-0.081434, 0.996546, -0.016286), (-0.008238, 0.015667, 0.999843)-6.65264, 59.42231, -43.6895
3given(0.984493, 0.175371, -0.004303), (0.175391, -0.984488, 0.004616), (-0.003427, -0.005299, -0.99998)-7.35918, 85.08093, 44.035

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Components

#1: Protein
CCDB


Mass: 11721.508 Da / Num. of mol.: 4
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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Dao-Thi, M.H., (1997) Acta Crystallog. sect D., 54, 975.
PH range low: 8.5 / PH range high: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.0-12.0 mg/mlprotein1drop
20.8-2.0 Mammonium sulfate1drop
30-2 %agarose1drop

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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: Aug 1, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→10 Å / Num. obs: 101106 / % possible obs: 93 % / Redundancy: 6.82 % / Rsym value: 0.098 / Net I/σ(I): 22.2
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.89 / Rsym value: 0.333 / % possible all: 77.6
Reflection
*PLUS
Num. obs: 14825 / Num. measured all: 101106 / Rmerge(I) obs: 0.098
Reflection shell
*PLUS
% possible obs: 77.6 % / Rmerge(I) obs: 0.333

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(ROTAVATA)data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PRELIMINARY MIR MODEL IN DIFFERENT CRYSTAL FORM

Resolution: 2.6→10 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1176 8 %RANDOM
Rwork0.199 ---
obs0.199 14825 93 %-
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 4 37 3225
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.518
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.19
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.372
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: 2.6→2.72 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3312 106 8 %
Rwork0.26 1308 -
obs--77.6 %
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_deg26.198
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.372
LS refinement shell
*PLUS
Rfactor Rwork: 0.26

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