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- PDB-6jay: Crystal structure of Ostrinia furnacalis Group II chitinase catal... -

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Basic information

Entry
Database: PDB / ID: 6jay
TitleCrystal structure of Ostrinia furnacalis Group II chitinase catalytic domain 1 in complex with a dipyrido-pyrimidine derivative
ComponentsGroup II chitinase
KeywordsHYDROLASE / inhibitor complex / 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
Chem-JUK / Group II chitinase
Similarity search - Component
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.498 Å
AuthorsChen, W. / Zhou, Y. / Yang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31425021 China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural dissection reveals a general mechanistic principle for group II chitinase (ChtII) inhibition.
Authors: Chen, W. / Zhou, Y. / Yang, Q.
History
DepositionJan 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 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 1.3Nov 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 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Group II chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1103
Polymers44,4681
Non-polymers6422
Water8,449469
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint3 kcal/mol
Surface area14450 Å2
Unit cell
Length a, b, c (Å)98.529, 98.529, 94.447
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Group II chitinase


Mass: 44468.395 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, chitinase
#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: Chemical ChemComp-JUK / 2-amino-1-[(furan-2-yl)methyl]-5-oxo-3-({[(2S)-oxolan-2-yl]methyl}carbamoyl)-5H-dipyrido[1,2-a:2',3'-d]pyrimidin-1-ium


Mass: 420.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H22N5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsThe residues 1863-1878 (GDKWDSPREQWRKDAN) seriously influenced its expression and crystallization, ...The residues 1863-1878 (GDKWDSPREQWRKDAN) seriously influenced its expression and crystallization, so they were replaced by ENRGIH, the corresponding residues in ChtII of Bombyx mori.

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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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M sodium chloride, 0.1M Tris (pH 8.5) and 25% PEG3350

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.498→50 Å / Num. obs: 133121 / % possible obs: 100 % / Redundancy: 14 % / Rsym value: 0.097 / Net I/σ(I): 5.8
Reflection shellResolution: 1.498→1.53 Å / Redundancy: 12.8 % / Num. unique obs: 3676 / Rsym value: 1.361 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y29

5y29


Resolution: 1.498→27.327 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1839 3658 2.75 %
Rwork0.173 --
obs0.1733 133115 93.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.498→27.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 45 469 3544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073181
X-RAY DIFFRACTIONf_angle_d1.0084330
X-RAY DIFFRACTIONf_dihedral_angle_d16.7731162
X-RAY DIFFRACTIONf_chiral_restr0.084439
X-RAY DIFFRACTIONf_plane_restr0.005549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4984-1.51810.2553840.22992907X-RAY DIFFRACTION54
1.5181-1.53890.229880.22423280X-RAY DIFFRACTION62
1.5389-1.56090.23511220.22663607X-RAY DIFFRACTION68
1.5609-1.58420.23661100.21124078X-RAY DIFFRACTION76
1.5842-1.6090.24891370.22014384X-RAY DIFFRACTION83
1.609-1.63530.23191100.21624840X-RAY DIFFRACTION91
1.6353-1.66350.21491590.21115103X-RAY DIFFRACTION95
1.6635-1.69380.23241350.21635237X-RAY DIFFRACTION98
1.6938-1.72630.27421540.19825329X-RAY DIFFRACTION100
1.7263-1.76160.22391430.19545348X-RAY DIFFRACTION100
1.7616-1.79990.21751560.18685295X-RAY DIFFRACTION100
1.7999-1.84170.16271350.17835327X-RAY DIFFRACTION100
1.8417-1.88780.19691560.17575368X-RAY DIFFRACTION100
1.8878-1.93880.19831410.17025325X-RAY DIFFRACTION100
1.9388-1.99580.17341590.16095337X-RAY DIFFRACTION100
1.9958-2.06020.15931510.16175318X-RAY DIFFRACTION100
2.0602-2.13390.14571600.16145359X-RAY DIFFRACTION100
2.1339-2.21930.18121560.16825315X-RAY DIFFRACTION100
2.2193-2.32020.18531470.16175339X-RAY DIFFRACTION100
2.3202-2.44250.20181430.16825324X-RAY DIFFRACTION100
2.4425-2.59540.1591510.16445356X-RAY DIFFRACTION100
2.5954-2.79560.17411610.16865327X-RAY DIFFRACTION100
2.7956-3.07660.18641450.17015337X-RAY DIFFRACTION100
3.0766-3.5210.17951450.16155346X-RAY DIFFRACTION100
3.521-4.4330.15061620.14935335X-RAY DIFFRACTION100
4.433-27.33160.18041480.17965336X-RAY DIFFRACTION100

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