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- PDB-7mtl: Crystal structure of colibactin self-resistance protein ClbS in c... -

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Basic information

Entry
Database: PDB / ID: 7mtl
TitleCrystal structure of colibactin self-resistance protein ClbS in complex with a dsDNA
Components
  • Colibactin self-protection protein ClbS
  • DNA (5'-D(*AP*AP*TP*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*AP*G)-3')
  • DNA (5'-D(*CP*TP*GP*GP*AP*AP*GP*TP*GP*GP*GP*AP*AP*TP*T)-3')
KeywordsDNA BINDING PROTEIN/DNA / hydrolase / DNA repair / DNA BINDING PROTEIN-DNA complex
Function / homologyProtein of unknown function DUF1706 / Protein of unknown function (DUF1706) / DinB/YfiT-like putative metalloenzymes / DNA / DNA (> 10) / Colibactin self-protection protein ClbS
Function and homology information
Biological speciesEscherichia coli (E. coli)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.446 Å
AuthorsTripathi, P. / Bruner, S.D.
Citation
Journal: Biochemistry / Year: 2021
Title: Structural Basis for the Interactions of the Colibactin Resistance Gene Product ClbS with DNA.
Authors: Tripathi, P. / Bruner, S.D.
#1: Journal: Journal of American Chemical Society / Year: 2017
Title: ClbS Is a Cyclopropane Hydrolase That Confers Colibactin Resistance
Authors: Tripathi, P. / Bruner, S.D.
History
DepositionMay 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Colibactin self-protection protein ClbS
B: Colibactin self-protection protein ClbS
C: DNA (5'-D(*AP*AP*TP*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*AP*G)-3')
D: DNA (5'-D(*CP*TP*GP*GP*AP*AP*GP*TP*GP*GP*GP*AP*AP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)50,6734
Polymers50,6734
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.783, 75.878, 178.326
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Colibactin self-protection protein ClbS


Mass: 20747.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: clbS, APU18_08100, AWF59_018730, AZZ83_004503, CT146_21495, CUB99_02165, D3C88_24730, DNR41_00045, DNX30_29170, DS966_21615, DU333_02935, DW236_02620, ELT23_23590, ELT33_24270, EPS70_02685, ...Gene: clbS, APU18_08100, AWF59_018730, AZZ83_004503, CT146_21495, CUB99_02165, D3C88_24730, DNR41_00045, DNX30_29170, DS966_21615, DU333_02935, DW236_02620, ELT23_23590, ELT33_24270, EPS70_02685, EPS94_00180, EWK56_23755, FPI65_12320, FQU83_11985, GFU47_04510, GP945_05010, GP946_20500, HHG54_004716, HHJ44_00090, HJL93_000008, HJM41_001166, HJO44_004707, HJS53_002303, HmCmsJML146_00176, HNX34_25610, HV055_09710, HV098_09980, HV348_09415, NCTC9075_02752, NCTC9434_01964
Production host: Escherichia coli (E. coli) / References: UniProt: Q0P7K8
#2: DNA chain DNA (5'-D(*AP*AP*TP*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*AP*G)-3')


Mass: 4488.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*TP*GP*GP*AP*AP*GP*TP*GP*GP*GP*AP*AP*TP*T)-3')


Mass: 4689.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate trihydrate pH 7.0, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.446→46.793 Å / Num. obs: 22255 / % possible obs: 99.86 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 11.79
Reflection shellResolution: 2.446→2.533 Å / Mean I/σ(I) obs: 1.44 / Num. unique obs: 2168 / CC1/2: 0.755 / % possible all: 98.77

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ANR

6anr


Resolution: 2.446→46.793 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2834 1173 5.28 %
Rwork0.2307 21050 -
obs0.2335 22223 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.75 Å2 / Biso mean: 64.8658 Å2 / Biso min: 29.3 Å2
Refinement stepCycle: final / Resolution: 2.446→46.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2703 609 0 10 3322
Biso mean---49.3 -
Num. residues----360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.446-2.55710.37781170.3375256699
2.5571-2.69190.40481590.30542565100
2.6919-2.86050.36521400.30742610100
2.8605-3.08140.37561570.28912579100
3.0814-3.39140.30731450.24962601100
3.3914-3.88190.30321540.23292641100
3.8819-4.890.23671370.19662677100
4.89-46.7930.23171640.19352811100

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