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- PDB-6t9m: Crystal structure of the Chitinase Domain of the Spore Coat Prote... -

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Basic information

Entry
Database: PDB / ID: 6t9m
TitleCrystal structure of the Chitinase Domain of the Spore Coat Protein CotE from Clostridium difficile
Components
  • Peptide in active site
  • Peroxiredoxin
KeywordsSTRUCTURAL PROTEIN / Spore Coat / Chitinase / Colonisation Factor
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin activity / chitinase activity / thioredoxin-dependent peroxiredoxin / chitin catabolic process / chitin binding / carbohydrate metabolic process / extracellular region / 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 ...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 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Peroxiredoxin
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
Escherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsWhittingham, J.L. / Dodson, E.J. / Wilkinson, A.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/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
DepositionOct 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Peroxiredoxin
BBB: Peptide in active site
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2237
Polymers43,4282
Non-polymers7955
Water8,827490
1
AAA: Peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7196
Polymers42,9241
Non-polymers7955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
BBB: Peptide in active site


  • defined by author&software
  • 504 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)5041
Polymers5041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.894, 54.899, 80.311
Angle α, β, γ (deg.)90.000, 101.038, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peroxiredoxin / Thioredoxin peroxidase


Mass: 42924.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This is the C-terminal chitinase domain of a bifunctional protein found in the spores of Clostridium difficile. It has an HRV 3C cleavable H6 tag fused to its N-terminus
Source: (gene. exp.) Peptoclostridium difficile (strain 630) (bacteria)
Strain: 630 / Gene: cotE, CD630_14330 / Plasmid: pETYSBLLIC3C
Details (production host): T7 promoter regulated by lac repressor/operator
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q18BV5, peroxiredoxin
#2: Protein/peptide Peptide in active site


Mass: 503.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: peptide defined by electron density in active site / Source: (synth.) Escherichia coli K-12 (bacteria)
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 490 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Well solution: 200 mM ammonium phosphate, 22.5% PEG 3350 Protein solution: 20 mM Tris-HCl, pH 8.0, 150 mM NaCl Drop: 3 microlitre (1 microlitre protein plus 2 microlitre reservoir solution)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→47.21 Å / Num. obs: 94650 / % possible obs: 97.9 % / Redundancy: 4.6 % / CC1/2: 0.997 / Rrim(I) all: 0.058 / Net I/σ(I): 18
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 6.5 / Num. unique obs: 4564 / CC1/2: 0.954 / Rrim(I) all: 0.31 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: xxx

Resolution: 1.3→45.09 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.137 / WRfactor Rwork: 0.107 / Average fsc free: 0.9794 / Average fsc work: 0.9835 / Cross valid method: FREE R-VALUE / ESU R: 0.034 / ESU R Free: 0.035
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1333 4557 4.83 %
Rwork0.1055 89793 -
all0.107 --
obs-94350 97.89 %
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: 14.194 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0.013 Å2
2--0.011 Å20 Å2
3----0.005 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2777 0 53 490 3320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0132999
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172719
X-RAY DIFFRACTIONr_angle_refined_deg2.4711.6434073
X-RAY DIFFRACTIONr_angle_other_deg2.4671.5736323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5185375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34922.919161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.20515469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3491518
X-RAY DIFFRACTIONr_chiral_restr0.1450.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023420
X-RAY DIFFRACTIONr_gen_planes_other0.0240.02638
X-RAY DIFFRACTIONr_nbd_refined0.2340.2609
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2180.22579
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21470
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21362
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2420.2331
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.5090.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4850.25
X-RAY DIFFRACTIONr_nbd_other0.2440.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3390.228
X-RAY DIFFRACTIONr_mcbond_it1.4221.1561476
X-RAY DIFFRACTIONr_mcbond_other1.3811.1531475
X-RAY DIFFRACTIONr_mcangle_it1.741.7381859
X-RAY DIFFRACTIONr_mcangle_other1.7551.741860
X-RAY DIFFRACTIONr_scbond_it2.9621.5231523
X-RAY DIFFRACTIONr_scbond_other2.9661.5251524
X-RAY DIFFRACTIONr_scangle_it3.1642.162214
X-RAY DIFFRACTIONr_scangle_other3.1632.1612215
X-RAY DIFFRACTIONr_lrange_it3.29416.7823562
X-RAY DIFFRACTIONr_lrange_other3.29416.793563
X-RAY DIFFRACTIONr_rigid_bond_restr10.42335718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.3340.1583280.1196466X-RAY DIFFRACTION96.1098
1.334-1.370.1353210.1016414X-RAY DIFFRACTION96.6561
1.37-1.410.1253030.096210X-RAY DIFFRACTION96.9629
1.41-1.4530.1122820.0816038X-RAY DIFFRACTION97.2607
1.453-1.5010.1062580.0745900X-RAY DIFFRACTION97.5911
1.501-1.5540.1073250.0735681X-RAY DIFFRACTION97.6268
1.554-1.6120.1012910.0655502X-RAY DIFFRACTION97.8547
1.612-1.6780.1142770.0735317X-RAY DIFFRACTION98.382
1.678-1.7530.1142810.0765141X-RAY DIFFRACTION98.6536
1.753-1.8380.1212290.0844928X-RAY DIFFRACTION98.2099
1.838-1.9380.1182370.094636X-RAY DIFFRACTION98.9643
1.938-2.0550.1362600.1014403X-RAY DIFFRACTION98.8552
2.055-2.1970.1152020.0984179X-RAY DIFFRACTION98.538
2.197-2.3730.1171860.13911X-RAY DIFFRACTION99.3694
2.373-2.5990.141980.1093567X-RAY DIFFRACTION99.1833
2.599-2.9050.1351540.123269X-RAY DIFFRACTION98.8735
2.905-3.3540.1511310.1252865X-RAY DIFFRACTION98.1009
3.354-4.1060.1361280.1262436X-RAY DIFFRACTION99.1109
4.106-5.7990.164960.1381890X-RAY DIFFRACTION98.3168
5.799-45.090.205700.1841040X-RAY DIFFRACTION96.0208

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