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- PDB-6g9e: Crystal structure of immunomodulatory active chitinase from Trich... -

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Basic information

Entry
Database: PDB / ID: 6g9e
TitleCrystal structure of immunomodulatory active chitinase from Trichuris suis - TsES1 - 6 molecules in ASU
ComponentsImmunomodulatory active chitinase
KeywordsHYDROLASE / TsES1 / immunomodulatory potential / chitinase / Eukaryotic protein expression / LEXSY / secretion / dimer / intramolecular disulphide bridge
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 ...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 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesTrichuris suis (pig whipworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 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 / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunomodulatory active chitinase
B: Immunomodulatory active chitinase
C: Immunomodulatory active chitinase
D: Immunomodulatory active chitinase
E: Immunomodulatory active chitinase
F: Immunomodulatory active chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,58411
Polymers333,2746
Non-polymers3105
Water8,161453
1
A: Immunomodulatory active chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6082
Polymers55,5461
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immunomodulatory active chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6082
Polymers55,5461
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Immunomodulatory active chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6703
Polymers55,5461
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Immunomodulatory active chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6082
Polymers55,5461
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Immunomodulatory active chitinase


Theoretical massNumber of molelcules
Total (without water)55,5461
Polymers55,5461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Immunomodulatory active chitinase


Theoretical massNumber of molelcules
Total (without water)55,5461
Polymers55,5461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)220.063, 172.618, 138.564
Angle α, β, γ (deg.)90.000, 128.410, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-684-

HOH

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Components

#1: Protein
Immunomodulatory active chitinase


Mass: 55545.691 Da / Num. of mol.: 6 / 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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O
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: 4.09 Å3/Da / Density % sol: 69.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 100mM Tris, 200mM Magnesium chloride hexahydrate, 10% PEG 8000

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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: 2.69→45.61 Å / Num. obs: 110673 / % possible obs: 99 % / Redundancy: 3.9 % / Biso Wilson estimate: 37.83 Å2 / CC1/2: 0.967 / Rmerge(I) obs: 0.267 / Rpim(I) all: 0.155 / Rrim(I) all: 0.31 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.69-2.743.71.30349520.4880.7671.51789.5
14.75-45.613.40.0666860.9910.0410.07995.6

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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: 2.69→45.61 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.44
RfactorNum. reflection% reflection
Rfree0.2491 1103 1 %
Rwork0.1925 --
obs0.193 110597 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.97 Å2 / Biso mean: 43.0582 Å2 / Biso min: 16.8 Å2
Refinement stepCycle: final / Resolution: 2.69→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17772 0 20 455 18247
Biso mean--54.99 35.4 -
Num. residues----2208
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.69-2.81560.37181460.30331313995
2.8156-2.9640.32161430.26351369399
2.964-3.14960.27171490.252513717100
3.1496-3.39280.2881930.22881367799
3.3928-3.7340.25141040.18671374199
3.734-4.2740.21141380.157513819100
4.274-5.38340.1803950.14121382599
5.3834-45.610.20471350.16981388399
Refinement TLS params.Method: refined / Origin x: 12.3924 Å / Origin y: 5.3288 Å / Origin z: 130.6447 Å
111213212223313233
T0.228 Å20.011 Å20.0427 Å2-0.2429 Å20.0009 Å2--0.2258 Å2
L0.5704 °20.0419 °20.0179 °2-0.3468 °2-0.0174 °2--0.2552 °2
S0.0099 Å °-0.1475 Å °0.0174 Å °0.1066 Å °-0.0045 Å °-0.0304 Å °-0.0105 Å °0.0152 Å °-0.0055 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA32 - 399
2X-RAY DIFFRACTION1allB32 - 399
3X-RAY DIFFRACTION1allC32 - 399
4X-RAY DIFFRACTION1allD32 - 399
5X-RAY DIFFRACTION1allE32 - 399
6X-RAY DIFFRACTION1allF32 - 399
7X-RAY DIFFRACTION1allG1 - 474
8X-RAY DIFFRACTION1allH1
9X-RAY DIFFRACTION1allH2
10X-RAY DIFFRACTION1allH3 - 5
11X-RAY DIFFRACTION1allH6

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