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- PDB-5y29: Crystal structure of Ostrinia furnacalis Group II chitinase catal... -

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Basic information

Entry
Database: PDB / ID: 5y29
TitleCrystal structure of Ostrinia furnacalis Group II chitinase catalytic domain 1
Componentsinsect group II chitinase
KeywordsHYDROLASE / GH18 chitinase
Function / homology
Function and homology information


endochitinase activity / chitinase / 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
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChen, W. / Qu, M.B. / Zhou, Y. / Yang, Q.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural analysis of group II chitinase (ChtII) catalysis completes the puzzle of chitin hydrolysis in insects
Authors: Chen, W. / Qu, M. / Zhou, Y. / Yang, Q.
History
DepositionJul 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: insect group II chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1612
Polymers42,9401
Non-polymers2211
Water6,161342
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint3 kcal/mol
Surface area14580 Å2
Unit cell
Length a, b, c (Å)98.529, 98.529, 93.957
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein insect group II chitinase


Mass: 42939.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Production host: Komagataella pastoris GS115 (fungus) / References: UniProt: A0A221ZS22*PLUS
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium chloride, 0.1M Tris, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 26, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 43489 / % possible obs: 100 % / Redundancy: 26.2 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.019 / Rrim(I) all: 0.097 / Χ2: 2.515 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8326.90.4444150.9860.0860.4481.547100
1.83-1.86270.3920.9890.0770.41.605100
1.86-1.9270.3310.9920.0650.3371.675100
1.9-1.9427.10.290.9920.0570.2961.75100
1.94-1.9827.20.2660.9940.0520.2711.788100
1.98-2.0327.10.2270.9960.0450.2311.877100
2.03-2.0827.10.2040.9960.040.2081.99100
2.08-2.1326.90.180.9970.0360.1842.075100
2.13-2.226.90.1610.9970.0320.1642.17100
2.2-2.2726.90.1510.9970.030.1542.247100
2.27-2.3526.70.1390.9980.0280.1422.404100
2.35-2.4426.80.1320.9980.0260.1342.566100
2.44-2.5526.40.1280.9980.0250.132.928100
2.55-2.6925.90.1210.9980.0240.1233.246100
2.69-2.8625.60.110.9980.0220.1123.427100
2.86-3.0824.90.0980.9980.020.13.728100
3.08-3.39250.0820.9990.0170.0843.76100
3.39-3.8824.10.0610.9990.0130.0623.213100
3.88-4.8825.70.0550.9990.0110.0563.203100
4.88-3024.10.060.9990.0130.0623.35299.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11_2567refinement
PDB_EXTRACT3.22data extraction
Cootmodel building
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GUV

1guv


Resolution: 1.8→30 Å / Cross valid method: NONE
RfactorNum. reflection% reflection
Rfree0.1985 1979 -
Rwork0.1802 --
obs-43489 100 %
Displacement parametersBiso max: 71.16 Å2 / Biso mean: 22.8843 Å2 / Biso min: 10.14 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 14 343 3380
LS refinement shellResolution: 1.7799→1.8244 Å
RfactorNum. reflection% reflection
Rfree0.2538 136 -
Rwork0.2142 3004 -
obs--99 %

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