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- PDB-7epi: Crystal structure of E.coli CcdB mutant S60E -

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Basic information

Entry
Database: PDB / ID: 7epi
TitleCrystal structure of E.coli CcdB mutant S60E
ComponentsToxin CcdB
KeywordsTOXIN / CcdB / Topoisomerase poison / global suppressor
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 / Plasmid maintenance toxin/Cell growth inhibitor
Similarity search - Domain/homology
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.931 Å
AuthorsManjunath, K. / Goyal, P. / Varadarajan, R.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/COE/34/SP15219/2015 India
Department of Science & Technology (DST, India) India
CitationJournal: Plos Genet. / Year: 2022
Title: Mechanistic insights into global suppressors of protein folding defects.
Authors: Chattopadhyay, G. / Bhowmick, J. / Manjunath, K. / Ahmed, S. / Goyal, P. / Varadarajan, R.
History
DepositionApr 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxin CcdB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8343
Polymers11,7641
Non-polymers712
Water1,76598
1
A: Toxin CcdB
hetero molecules

A: Toxin CcdB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6696
Polymers23,5272
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2120 Å2
ΔGint-19 kcal/mol
Surface area10510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.810, 36.640, 35.670
Angle α, β, γ (deg.)90.000, 114.970, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

21A-486-

HOH

31A-498-

HOH

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Components

#1: Protein Toxin CcdB / Cytotoxic protein CcdB / LynB / Protein G / Protein LetD


Mass: 11763.544 Da / Num. of mol.: 1 / Mutation: S60E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: ccdB, G, letB, letD, ECOK12F043 / Plasmid: pBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10Gyrase / References: UniProt: P62554
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.9 Å3/Da / Density % sol: 35.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 200mM CaCl2, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→10 Å / Num. obs: 6557 / % possible obs: 97.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 8.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.081 / Rrim(I) all: 0.154 / Net I/σ(I): 9.6
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 890 / CC1/2: 0.801 / Rpim(I) all: 0.268 / Rrim(I) all: 0.504 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VUB

3vub


Resolution: 1.931→9.996 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.194 / WRfactor Rwork: 0.151 / SU B: 3.531 / SU ML: 0.102 / Average fsc free: 0.9302 / Average fsc work: 0.9486 / Cross valid method: FREE R-VALUE / ESU R: 0.202 / ESU R Free: 0.162
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2135 333 5.079 %
Rwork0.1697 6224 -
all0.172 --
obs-6557 97.807 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 10.319 Å2
Baniso -1Baniso -2Baniso -3
1--0.006 Å2-0 Å2-0.372 Å2
2--0.359 Å2-0 Å2
3----0.005 Å2
Refinement stepCycle: LAST / Resolution: 1.931→9.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms803 0 2 98 903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.013837
X-RAY DIFFRACTIONr_bond_other_d0.0010.017794
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.6461133
X-RAY DIFFRACTIONr_angle_other_deg1.1571.5771833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4525101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.93620.40849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58415156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.731159
X-RAY DIFFRACTIONr_chiral_restr0.0580.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02924
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02187
X-RAY DIFFRACTIONr_nbd_refined0.1870.2140
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.2771
X-RAY DIFFRACTIONr_nbtor_refined0.1540.2399
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2377
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.271
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2620.224
X-RAY DIFFRACTIONr_nbd_other0.2130.288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.216
X-RAY DIFFRACTIONr_mcbond_it0.7561.013398
X-RAY DIFFRACTIONr_mcbond_other0.7181.006397
X-RAY DIFFRACTIONr_mcangle_it1.3571.5495
X-RAY DIFFRACTIONr_mcangle_other1.3631.506496
X-RAY DIFFRACTIONr_scbond_it0.7021.065439
X-RAY DIFFRACTIONr_scbond_other0.691.065439
X-RAY DIFFRACTIONr_scangle_it1.2161.568636
X-RAY DIFFRACTIONr_scangle_other1.2161.567636
X-RAY DIFFRACTIONr_lrange_it3.33511.782947
X-RAY DIFFRACTIONr_lrange_other3.11711.47925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.931-1.9810.259190.246450X-RAY DIFFRACTION94.5564
1.981-2.0350.235220.175437X-RAY DIFFRACTION98.2869
2.035-2.0940.179350.182416X-RAY DIFFRACTION98.2571
2.094-2.1580.176260.164420X-RAY DIFFRACTION98.022
2.158-2.2290.281290.157405X-RAY DIFFRACTION98.19
2.229-2.3070.194120.178406X-RAY DIFFRACTION98.3529
2.307-2.3930.245210.154373X-RAY DIFFRACTION98.995
2.393-2.4910.198200.164369X-RAY DIFFRACTION98.731
2.491-2.6010.17140.152367X-RAY DIFFRACTION98.7047
2.601-2.7270.165160.153335X-RAY DIFFRACTION98.8732
2.727-2.8730.199180.154327X-RAY DIFFRACTION99.4236
2.873-3.0460.236110.151318X-RAY DIFFRACTION100
3.046-3.2550.297210.141291X-RAY DIFFRACTION100
3.255-3.5130.141180.143263X-RAY DIFFRACTION100
3.513-3.8440.206150.156254X-RAY DIFFRACTION100
3.844-4.2910.235120.13236X-RAY DIFFRACTION100
4.291-4.9410.192130.125198X-RAY DIFFRACTION100
4.941-6.020.16430.192188X-RAY DIFFRACTION99.4792
6.02-8.3820.32780.305136X-RAY DIFFRACTION99.3103
8.382-9.99608.44635X-RAY DIFFRACTION38.8889

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