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- PDB-8hw7: Crystal structure of Heterodera glycines chitinase 2 D129A/E131A ... -

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Basic information

Entry
Database: PDB / ID: 8hw7
TitleCrystal structure of Heterodera glycines chitinase 2 D129A/E131A mutant in complex with chitopentaose
ComponentsChitinase
KeywordsHYDROLASE / chitinase
Function / homology
Function and homology information


chitin binding / carbohydrate metabolic process
Similarity search - Function
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
Biological speciesHeterodera glycines (soybean cyst nematode)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChen, W. / Chen, Q. / Wang, D. / Yang, Q.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31830076 China
National Natural Science Foundation of China (NSFC)32161133010 China
National Natural Science Foundation of China (NSFC)32272595 China
CitationJournal: Nat Microbiol / Year: 2024
Title: A soybean cyst nematode suppresses microbial plant symbionts using a lipochitooligosaccharide-hydrolysing enzyme.
Authors: Chen, W. / Wang, D. / Ke, S. / Cao, Y. / Xiang, W. / Guo, X. / Yang, Q.
History
DepositionDec 29, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Dec 18, 2024Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7383
Polymers39,2801
Non-polymers1,4582
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint27 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.911, 69.599, 50.685
Angle α, β, γ (deg.)90.00, 105.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chitinase


Mass: 39279.551 Da / Num. of mol.: 1 / Mutation: D129A,E131A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heterodera glycines (soybean cyst nematode)
Production host: Komagataella pastoris (fungus) / References: UniProt: Q8I6X8, chitinase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: 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: obtained synthetically
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.03 Å3/Da / Density % sol: 39.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M ammonium acetate, 0.1 M Bis-tris, pH 5.5, and 20% PEG 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.746→30 Å / Num. obs: 31892 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 16.64 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 10.58
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.4613 / Num. unique obs: 3077 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→29.62 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.181 1995 6.26 %
Rwork0.152 --
obs0.154 31847 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2504 0 99 398 3001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142681
X-RAY DIFFRACTIONf_angle_d1.7473645
X-RAY DIFFRACTIONf_dihedral_angle_d9.0421535
X-RAY DIFFRACTIONf_chiral_restr0.238417
X-RAY DIFFRACTIONf_plane_restr0.008450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.23671370.20172029X-RAY DIFFRACTION96
1.79-1.83830.22471330.1922106X-RAY DIFFRACTION100
1.8383-1.89240.20621450.16662161X-RAY DIFFRACTION100
1.8924-1.95350.22381420.15772156X-RAY DIFFRACTION100
1.9535-2.02330.17551440.15072091X-RAY DIFFRACTION100
2.0233-2.10430.19271400.14662151X-RAY DIFFRACTION100
2.1043-2.20.17541480.14262143X-RAY DIFFRACTION100
2.2-2.3160.19831490.15142120X-RAY DIFFRACTION100
2.316-2.4610.17421420.15152137X-RAY DIFFRACTION100
2.461-2.65090.20761480.15732131X-RAY DIFFRACTION100
2.6509-2.91750.18651330.15682151X-RAY DIFFRACTION100
2.9175-3.33920.17961480.15312168X-RAY DIFFRACTION100
3.3392-4.20510.14261410.13082156X-RAY DIFFRACTION100
4.2051-100.17151450.15652152X-RAY DIFFRACTION98

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