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- PDB-6g9c: Crystal structure of immunomodulatory active chitinase from Trich... -

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Basic information

Entry
Database: PDB / ID: 6g9c
TitleCrystal structure of immunomodulatory active chitinase from Trichuris suis, TsES1
ComponentsImmunomodulatory active chitinase
KeywordsHYDROLASE / TsES1 / immunomodulatory potential / chitinase / Eukaryotic protein expression / LEXSY / secretion / dimer / intramolecular disulphide bridge / Trichuris suis
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin 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 ...Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin 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 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chitin-binding type-2 domain-containing protein
Similarity search - Component
Biological speciesTrichuris suis (pig whipworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsMalecki, P.H. / Balster, K. / Hartmann, S. / Weiss, M.S. / Heinemann, U.
CitationJournal: J Immunol Res / Year: 2021
Title: A Helminth-Derived Chitinase Structurally Similar to Mammalian Chitinase Displays Immunomodulatory Properties in Inflammatory Lung Disease.
Authors: Ebner, F. / Lindner, K. / Janek, K. / Niewienda, A. / Malecki, P.H. / Weiss, M.S. / Sutherland, T.E. / Heuser, A. / Kuhl, A.A. / Zentek, J. / Hofmann, A. / Hartmann, S.
History
DepositionApr 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunomodulatory active chitinase
B: Immunomodulatory active chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,77413
Polymers111,0912
Non-polymers68311
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint26 kcal/mol
Surface area28290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.083, 52.613, 93.450
Angle α, β, γ (deg.)90.000, 108.790, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Immunomodulatory active chitinase


Mass: 55545.691 Da / Num. of mol.: 2 / Fragment: TsES1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichuris suis (pig whipworm) / Gene: M513_10624 / Production host: Leishmania tarentolae (eukaryote) / References: UniProt: A0A085LU44
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 100mM Bis_Tris, 200mM Ammonium sulfate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2017
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.74→46.41 Å / Num. obs: 92411 / % possible obs: 99.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 30.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.038 / Rrim(I) all: 0.093 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.74-1.775.42.42745060.3221.1292.68599.3
9.53-46.415.20.0246220.9980.0110.02698.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.6.2data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5hbf

5hbf


Resolution: 1.74→46.115 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.69
RfactorNum. reflection% reflection
Rfree0.2049 1997 2.16 %
Rwork0.1751 --
obs0.1757 92304 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.91 Å2 / Biso mean: 40.1235 Å2 / Biso min: 20.51 Å2
Refinement stepCycle: final / Resolution: 1.74→46.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5924 0 44 517 6485
Biso mean--47.33 47.23 -
Num. residues----736
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.74-1.78350.3951410.38656354649599
1.7835-1.83180.32791400.3356388652899
1.8318-1.88570.3341440.291864456589100
1.8857-1.94650.28981410.2576420656199
1.9465-2.01610.25471420.240864036545100
2.0161-2.09680.27581420.21946430657299
2.0968-2.19230.2521430.18766439658299
2.1923-2.30780.2061410.176764296570100
2.3078-2.45240.22051430.17436445658899
2.4524-2.64170.19741420.17316436657899
2.6417-2.90760.20281440.16766498664299
2.9076-3.32820.1981440.170864906634100
3.3282-4.19270.16831420.14436456659898
4.1927-46.13090.17271480.14666674682299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0407-0.8119-1.20081.12840.39551.88910.0067-0.084-0.07640.0717-0.0017-0.0442-0.07810.0715-0.00690.1961-0.0001-0.01070.17340.00610.18168.041139.86245.8527
21.63790.13531.09011.09470.39882.8778-0.02450.0717-0.0055-0.00680.0548-0.15580.02540.3685-0.03190.24970.02870.00440.2499-0.01330.210682.653515.9254-36.8
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 42:399)A42 - 399
2X-RAY DIFFRACTION2(chain B and resseq 42:399)B42 - 399

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