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

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Basic information

Entry
Database: PDB / ID: 7mtt
TitleCrystal structure of colibactin self-resistance protein ClbS in complex with two molecules of CHES
ComponentsColibactin self-protection protein ClbS
KeywordsDNA BINDING PROTEIN / hydrolase / DNA repair
Function / homologyProtein of unknown function DUF1706 / Protein of unknown function (DUF1706) / DinB/YfiT-like putative metalloenzymes / Colibactin self-protection protein ClbS
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

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Assembly

Deposited unit
A: Colibactin self-protection protein ClbS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1623
Polymers20,7481
Non-polymers4152
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.545, 60.173, 66.497
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.: 1
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: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 52.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CHES, pH 9.5, and 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1.033 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: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.85→44.62 Å / Num. obs: 17844 / % possible obs: 99.58 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 19.4
Reflection shellResolution: 1.85→1.915 Å / Num. unique obs: 1713 / CC1/2: 0.961

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ANR

6anr


Resolution: 1.85→44.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.265 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 934 5.2 %RANDOM
Rwork0.1902 ---
obs0.1922 16871 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.59 Å2 / Biso mean: 36.132 Å2 / Biso min: 19.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2---3 Å20 Å2
3---1.91 Å2
Refinement stepCycle: final / Resolution: 1.85→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 26 50 1457
Biso mean--54.31 33.81 -
Num. residues----169
LS refinement shellResolution: 1.85→1.897 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.332 66 -
Rwork0.265 1198 -
obs--96.93 %

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