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- PDB-8hw8: Crystal structure of Heterodera glycines chitinase 2 D129A/E131A ... -

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Basic information

Entry
Database: PDB / ID: 8hw8
TitleCrystal structure of Heterodera glycines chitinase 2 D129A/E131A mutant in complex with nodulation factor SmNF-V (C16:2, S)
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
: / DI(HYDROXYETHYL)ETHER / Chitinase
Similarity search - Component
Biological speciesHeterodera glycines (soybean cyst nematode)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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 1.1Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1345
Polymers39,2801
Non-polymers1,8554
Water5,170287
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.005, 69.384, 50.818
Angle α, β, γ (deg.)90.00, 105.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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

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Sugars , 2 types, 2 molecules

#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-6-O-sulfo-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.849 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAc[6S]b1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O_6*OSO/3=O/3=O][a2122h-1b_1-5_2*NCC/3=O]/1-2-2-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc6SO3]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-4-deoxy-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: 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: obtained synthetically
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

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Non-polymers , 3 types, 289 molecules

#4: Chemical ChemComp-68X / (2~{Z},9~{E})-~{N}-[(2~{R},3~{S},4~{R},5~{S},6~{S})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]hexadeca-2,9-dienamide


Mass: 413.548 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H39NO6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.04 Å3/Da / Density % sol: 39.58 %
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: 1.57→29.65 Å / Num. obs: 43220 / % possible obs: 98 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.47 Å2 / Rmerge(I) obs: 0.06299 / Rsym value: 0.06815 / Net I/σ(I): 15.09
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.5986 / Mean I/σ(I) obs: 2.21 / Num. unique obs: 4267 / % possible all: 98

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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: 1.57→29.65 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.187 1993 4.61 %
Rwork0.169 --
obs0.17 43219 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.57→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 124 287 2913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072705
X-RAY DIFFRACTIONf_angle_d1.2273668
X-RAY DIFFRACTIONf_dihedral_angle_d10.7881561
X-RAY DIFFRACTIONf_chiral_restr0.061414
X-RAY DIFFRACTIONf_plane_restr0.006454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.60880.29611390.21262868X-RAY DIFFRACTION96
1.6088-1.65230.22461340.20532936X-RAY DIFFRACTION98
1.6523-1.70090.2071370.19452924X-RAY DIFFRACTION98
1.7009-1.75580.21361500.18442949X-RAY DIFFRACTION98
1.7558-1.81860.21671550.17952930X-RAY DIFFRACTION98
1.8186-1.89140.2051210.17952860X-RAY DIFFRACTION95
1.8914-1.97750.19381450.17912934X-RAY DIFFRACTION99
1.9775-2.08170.19191490.16882950X-RAY DIFFRACTION99
2.0817-2.21210.19591480.16822987X-RAY DIFFRACTION99
2.2121-2.38280.2161410.17912897X-RAY DIFFRACTION97
2.3828-2.62250.17761480.17762995X-RAY DIFFRACTION99
2.6225-3.00160.20311400.1713004X-RAY DIFFRACTION99
3.0016-3.78050.15871400.15862954X-RAY DIFFRACTION98
3.7805-100.17131460.15573038X-RAY DIFFRACTION99

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