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- PDB-6tsb: Crystal structure of the Chitinase Domain of the Spore Coat Prote... -

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Basic information

Entry
Database: PDB / ID: 6tsb
TitleCrystal structure of the Chitinase Domain of the Spore Coat Protein CotE from Clostridium difficile
ComponentsPeroxiredoxin
KeywordsSTRUCTURAL PROTEIN / Spore Coat / Chitinase / Colonisation Factor
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin activity / thioredoxin-dependent peroxiredoxin / chitin binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Peroxiredoxin, TDXH subfamily / 1-Cys peroxiredoxin / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II ...Peroxiredoxin, TDXH subfamily / 1-Cys peroxiredoxin / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Peroxiredoxin
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWhittingham, J.L. / Dodson, E.J. / Wilkinson, A.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J007900/1 United Kingdom
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structures of the GH18 domain of the bifunctional peroxiredoxin-chitinase CotE from Clostridium difficile.
Authors: Whittingham, J.L. / Hanai, S. / Brannigan, J.A. / Ferreira, W.T. / Dodson, E.J. / Turkenburg, J.P. / Cartwright, J. / Cutting, S.M. / Wilkinson, A.J.
#1: Journal: J. Infect. Dis. / Year: 2017
Title: The Spore Coat Protein CotE Facilitates Host Colonization by Clostridium difficile.
Authors: Hong, H.A. / Ferreira, W.T. / Hosseini, S. / Anwar, S. / Hitri, K. / Wilkinson, A.J. / Vahjen, W. / Zentek, J. / Soloviev, M. / Cutting, S.M.
History
DepositionDec 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9843
Polymers40,7721
Non-polymers2122
Water2,486138
1
AAA: Peroxiredoxin
hetero molecules

AAA: Peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9686
Polymers81,5432
Non-polymers4244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area14710 Å2
ΔGint-82 kcal/mol
Surface area26880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.076, 82.076, 325.883
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11AAA-1003-

HOH

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Components

#1: Protein Peroxiredoxin / Thioredoxin peroxidase


Mass: 40771.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (strain 630) (bacteria)
Gene: cotE, CD630_14330 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q18BV5, peroxiredoxin
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.89 Å3/Da / Density % sol: 68.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Reservoir, 1 ml 0.1 M sodium malonate pH 5.5, 13% PEG 3,350 and 3 microlitres of pentaethylene glycol monooctyl ether (C8E5) Drops contained 2 microlitres of protein at 20 mg/ml in 50 mM ...Details: Reservoir, 1 ml 0.1 M sodium malonate pH 5.5, 13% PEG 3,350 and 3 microlitres of pentaethylene glycol monooctyl ether (C8E5) Drops contained 2 microlitres of protein at 20 mg/ml in 50 mM Tris-HCl, pH 7.5, 500 mM NaCl, 10 mM imidazole, a 3 microlitres of reservoir solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.17→81.41 Å / Num. obs: 35657 / % possible obs: 100 % / Redundancy: 18.3 % / CC1/2: 1 / Net I/σ(I): 9.5
Reflection shellResolution: 2.17→2.17 Å / Num. unique obs: 2551 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T9M

6t9m


Resolution: 2.1→54.373 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: FREE R-VALUE / ESU R: 0.153 / ESU R Free: 0.158
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2674 1918 4.894 %
Rwork0.2163 --
all0.219 --
obs-39192 99.957 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.348 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å2-0.001 Å2-0 Å2
2---0.001 Å20 Å2
3---0.005 Å2
Refinement stepCycle: LAST / Resolution: 2.1→54.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2699 0 14 138 2851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132771
X-RAY DIFFRACTIONr_bond_other_d0.0360.0172503
X-RAY DIFFRACTIONr_angle_refined_deg1.641.643764
X-RAY DIFFRACTIONr_angle_other_deg2.3761.5725806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4835344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31723.158152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8115436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7171516
X-RAY DIFFRACTIONr_chiral_restr0.0710.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023159
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02589
X-RAY DIFFRACTIONr_nbd_refined0.2120.2554
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.22263
X-RAY DIFFRACTIONr_nbtor_refined0.170.21308
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.21205
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2630.2113
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0970.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1750.261
X-RAY DIFFRACTIONr_nbd_other0.2470.2155
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3380.225
X-RAY DIFFRACTIONr_mcbond_it4.8475.6781379
X-RAY DIFFRACTIONr_mcbond_other4.8475.6761378
X-RAY DIFFRACTIONr_mcangle_it7.0178.51722
X-RAY DIFFRACTIONr_mcangle_other7.0168.5021723
X-RAY DIFFRACTIONr_scbond_it4.9036.0391392
X-RAY DIFFRACTIONr_scbond_other4.9016.041393
X-RAY DIFFRACTIONr_scangle_it7.2188.92042
X-RAY DIFFRACTIONr_scangle_other7.2168.9022043
X-RAY DIFFRACTIONr_lrange_it30.866.0713027
X-RAY DIFFRACTIONr_lrange_other30.79766.0863028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1540.4261540.4082679X-RAY DIFFRACTION99.9295
2.154-2.2130.4021200.3872615X-RAY DIFFRACTION100
2.213-2.2780.3791270.3732557X-RAY DIFFRACTION100
2.278-2.3480.3671360.3322465X-RAY DIFFRACTION100
2.348-2.4240.331250.3082405X-RAY DIFFRACTION100
2.424-2.5090.3351200.2792339X-RAY DIFFRACTION100
2.509-2.6040.3081220.2632246X-RAY DIFFRACTION100
2.604-2.710.3051090.2622193X-RAY DIFFRACTION100
2.71-2.8310.341160.2592104X-RAY DIFFRACTION100
2.831-2.9680.2961240.2291982X-RAY DIFFRACTION100
2.968-3.1290.26840.2251924X-RAY DIFFRACTION100
3.129-3.3180.3920.2241839X-RAY DIFFRACTION100
3.318-3.5470.267710.2121745X-RAY DIFFRACTION100
3.547-3.830.261810.1991612X-RAY DIFFRACTION100
3.83-4.1940.208740.1711508X-RAY DIFFRACTION100
4.194-4.6870.215590.1641378X-RAY DIFFRACTION100
4.687-5.4090.22690.1621231X-RAY DIFFRACTION100
5.409-6.6150.21560.1661060X-RAY DIFFRACTION100
6.615-9.3140.18490.138857X-RAY DIFFRACTION100
9.314-54.3730.296300.225535X-RAY DIFFRACTION98.7762

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