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- PDB-7epg: Crystal structure of E.coli CcdB mutant S12G -

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Basic information

Entry
Database: PDB / ID: 7epg
TitleCrystal structure of E.coli CcdB mutant S12G
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: 1.631 Å
AuthorsManjunath, K. / 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)11,7623
Polymers11,6911
Non-polymers712
Water1,71195
1
A: Toxin CcdB
hetero molecules

A: Toxin CcdB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5256
Polymers23,3832
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2010 Å2
ΔGint-17 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.570, 36.530, 67.528
Angle α, β, γ (deg.)90.000, 93.691, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-395-

HOH

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Components

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


Mass: 11691.482 Da / Num. of mol.: 1 / Mutation: S12G
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.: 95 / 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: 1.87 Å3/Da / Density % sol: 34.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.15 M CaCl2.2H2O, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→33.69 Å / Num. obs: 9822 / % possible obs: 90.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 11.66 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.041 / Rrim(I) all: 0.093 / Net I/σ(I): 9.8
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 1360 / CC1/2: 0.967 / Rpim(I) all: 0.097 / Rrim(I) all: 0.218 / % possible all: 86.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VUB

3vub


Resolution: 1.631→33.69 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.911 / SU B: 2.362 / SU ML: 0.088 / Cross valid method: FREE R-VALUE / ESU R: 0.156 / ESU R Free: 0.144
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2694 455 4.632 %0
Rwork0.2276 9367 --
all0.23 ---
obs-9822 89.92 %-
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: 17.012 Å2
Baniso -1Baniso -2Baniso -3
1--0.381 Å2-0 Å20.446 Å2
2--0.702 Å2-0 Å2
3----0.375 Å2
Refinement stepCycle: LAST / Resolution: 1.631→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms792 0 2 95 889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.013835
X-RAY DIFFRACTIONr_bond_other_d0.0010.017786
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.6441135
X-RAY DIFFRACTIONr_angle_other_deg1.2531.5761814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2885105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.12720.65246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17315148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.491158
X-RAY DIFFRACTIONr_chiral_restr0.0580.2112
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02927
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02185
X-RAY DIFFRACTIONr_nbd_refined0.2020.2163
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.2792
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2396
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2397
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.274
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2660.226
X-RAY DIFFRACTIONr_nbd_other0.2560.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1170.212
X-RAY DIFFRACTIONr_mcbond_it1.4161.734405
X-RAY DIFFRACTIONr_mcbond_other1.3851.731403
X-RAY DIFFRACTIONr_mcangle_it2.2632.6506
X-RAY DIFFRACTIONr_mcangle_other2.2452.599506
X-RAY DIFFRACTIONr_scbond_it1.4031.816430
X-RAY DIFFRACTIONr_scbond_other1.4011.817431
X-RAY DIFFRACTIONr_scangle_it2.2942.649626
X-RAY DIFFRACTIONr_scangle_other2.2932.65627
X-RAY DIFFRACTIONr_lrange_it4.62920.841966
X-RAY DIFFRACTIONr_lrange_other4.49720.307937
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.631-1.6730.332380.3296370.3297870.9560.97185.76870.325
1.673-1.7190.374340.2696480.2737850.8870.9286.8790.261
1.719-1.7690.3250.2676400.2687550.8490.82388.07950.258
1.769-1.8230.265260.2496360.257480.7930.80888.50270.246
1.823-1.8830.306370.2686010.277210.7460.79988.48820.267
1.883-1.9480.409340.4065440.4066760.7740.78985.5030.385
1.948-2.0220.226400.2415540.246600.8110.819900.256
2.022-2.1040.262250.2915600.296530.8050.82289.58650.299
2.104-2.1970.21590.2235560.2236230.9290.84990.69020.249
2.197-2.3040.455160.3655060.3695940.8510.85487.87880.35
2.304-2.4280.282300.2124870.2165640.8420.89491.66670.243
2.428-2.5740.253310.1934600.1965310.9080.92292.4670.223
2.574-2.7510.269320.1984310.2035000.9160.93292.60.232
2.751-2.970.185140.1684250.1694690.9520.94693.60340.206
2.97-3.2510.221190.1813860.1834300.940.94794.1860.222
3.251-3.630.22370.1453650.1473990.980.96393.23310.184
3.63-4.1840.228160.1623080.1653440.9550.96394.1860.195
4.184-5.1040.2120.1642780.1663080.9760.97294.15580.197
5.104-7.1370.15880.2452130.2412330.960.93894.84980.314
7.137-33.6940.5120.2461310.251420.9520.95193.6620.293

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