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- PDB-6anr: Crystal structure of a self resistance protein ClbS from colibact... -

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Basic information

Entry
Database: PDB / ID: 6anr
TitleCrystal structure of a self resistance protein ClbS from colibactin biosynthetic gene cluster
ComponentsColibactin self-protection protein ClbS
KeywordsHYDROLASE / Self resistance protein
Function / homologyProtein of unknown function DUF1706 / Protein of unknown function (DUF1706) / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Colibactin self-protection protein ClbS
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å
AuthorsTripathi, P. / Bruner, S.D.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: ClbS Is a Cyclopropane Hydrolase That Confers Colibactin Resistance.
Authors: Tripathi, P. / Shine, E.E. / Healy, A.R. / Kim, C.S. / Herzon, S.B. / Bruner, S.D. / Crawford, J.M.
History
DepositionAug 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Oct 4, 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


Theoretical massNumber of molelcules
Total (without water)20,7481
Polymers20,7481
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.458, 51.636, 71.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Colibactin self-protection protein ClbS / Putative uncharacterized protein


Mass: 20747.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: A4T50_02585, APU18_08100, WM48_10435 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0P7K8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.02 Å3/Da / Density % sol: 39.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.098→38.37 Å / Num. obs: 10332 / % possible obs: 99.89 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.0968 / Net I/σ(I): 25.37
Reflection shellResolution: 2.098→2.173 Å / Redundancy: 14 % / Rmerge(I) obs: 0.4939 / Num. unique obs: 1014 / % possible all: 98.93

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Cootmodel building
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N6C

4n6c


Resolution: 2.098→38.37 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.53
RfactorNum. reflection% reflection
Rfree0.2368 514 4.98 %
Rwork0.1803 --
obs0.1831 10329 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.098→38.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 0 148 1529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081408
X-RAY DIFFRACTIONf_angle_d1.011901
X-RAY DIFFRACTIONf_dihedral_angle_d14.678528
X-RAY DIFFRACTIONf_chiral_restr0.044203
X-RAY DIFFRACTIONf_plane_restr0.005241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.098-2.30910.23181350.17082389X-RAY DIFFRACTION100
2.3091-2.64320.27581140.19172426X-RAY DIFFRACTION100
2.6432-3.32980.27361390.18062428X-RAY DIFFRACTION100
3.3298-38.37860.19551260.17862572X-RAY DIFFRACTION100

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