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- PDB-8oye: Clostridium perfringens chitinase CP4_3455 E196Q with chitin -

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Basic information

Entry
Database: PDB / ID: 8oye
TitleClostridium perfringens chitinase CP4_3455 E196Q with chitin
ComponentsChitodextrinase
KeywordsHYDROLASE / chitinase / TIM / substrate / necrotic enteritis
Function / homology
Function and homology information


chitin catabolic process / chitin binding / polysaccharide binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Chitinase, C-terminal / Chitinase C / Immunoglobulin-like - #290 / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily / Chitinase II ...Chitinase, C-terminal / Chitinase C / Immunoglobulin-like - #290 / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / 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 / Glycoside hydrolase superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBloch, Y. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)12S0519N Belgium
CitationJournal: Plos Pathog. / Year: 2024
Title: Clostridium perfringens chitinases, key enzymes during early stages of necrotic enteritis in broiler chickens.
Authors: Dierick, E. / Callens, C. / Bloch, Y. / Savvides, S.N. / Hark, S. / Pelzer, S. / Ducatelle, R. / Van Immerseel, F. / Goossens, E.
History
DepositionMay 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Nov 13, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitodextrinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2843
Polymers65,1721
Non-polymers1,1122
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint24 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.486, 111.599, 108.916
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Chitodextrinase


Mass: 65171.520 Da / Num. of mol.: 1 / Mutation: E196Q active site mutant
Source method: isolated from a genetically manipulated source
Details: Residues [1-2] (MG) cloning scar / start codon. Truncated construct compared to WT. Residues [569-] (SHHHHHH) cloning scar and purification tag. Present during crystallization.
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: CP4_3455 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express lysY/Iq / References: UniProt: F8UNI5
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1033.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: PEGION A1: 0.2 M Sodium fluoride 20% w/v Polyethylene glycol 3,350, 1mM chitin hexamer (seeded)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.35→77.95 Å / Num. obs: 134505 / % possible obs: 99.3 % / Redundancy: 12.01 % / Biso Wilson estimate: 17.66 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.058 / Net I/σ(I): 23.82
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
4.05-77.9511.6651.9153280.9960.05398.7
1.43-1.5311.227.42204110.9690.36299.9
1.35-1.436.9563.4208920.8610.59796.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS20220820data reduction
XDSdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→77.95 Å / SU ML: 0.1176 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.4072
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1612 2016 1.5 %
Rwork0.1472 132482 -
obs0.1474 134498 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.27 Å2
Refinement stepCycle: LAST / Resolution: 1.35→77.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4472 0 75 576 5123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00454876
X-RAY DIFFRACTIONf_angle_d0.84436655
X-RAY DIFFRACTIONf_chiral_restr0.0703730
X-RAY DIFFRACTIONf_plane_restr0.0061857
X-RAY DIFFRACTIONf_dihedral_angle_d13.21191776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.2731330.26338769X-RAY DIFFRACTION93.07
1.38-1.420.17951440.18879256X-RAY DIFFRACTION98.58
1.42-1.460.18381490.14699427X-RAY DIFFRACTION99.7
1.46-1.510.19711360.12899424X-RAY DIFFRACTION99.95
1.51-1.560.14831420.12329469X-RAY DIFFRACTION99.99
1.56-1.630.15771590.11949438X-RAY DIFFRACTION99.97
1.63-1.70.18441440.12569457X-RAY DIFFRACTION99.97
1.7-1.790.16111160.12879509X-RAY DIFFRACTION99.97
1.79-1.90.17861570.12999483X-RAY DIFFRACTION99.97
1.9-2.050.16311750.13779478X-RAY DIFFRACTION99.98
2.05-2.260.15021170.13649558X-RAY DIFFRACTION99.94
2.26-2.580.15191160.13859628X-RAY DIFFRACTION99.99
2.58-3.250.18662120.15589608X-RAY DIFFRACTION99.96
3.25-77.950.12811160.15799978X-RAY DIFFRACTION99.2

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