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

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Basic information

Entry
Database: PDB / ID: 6jaw
TitleCrystal structure of Ostrinia furnacalis Group II chitinase catalytic domain 1 in complex with a napthalimide 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-BBO / Group II chitinase
Similarity search - Component
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 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 1.4Oct 16, 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)45,0143
Polymers44,4681
Non-polymers5462
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint3 kcal/mol
Surface area14320 Å2
Unit cell
Length a, b, c (Å)98.314, 98.314, 94.053
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: Chemical ChemComp-BBO / 2-[3-(morpholin-4-yl)propyl]-1H-benzo[de]isoquinoline-1,3(2H)-dione


Mass: 324.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.56 Å3/Da / Density % sol: 51.87 %
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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.981→50 Å / Num. obs: 51402 / % possible obs: 100 % / Redundancy: 12.7 % / Rsym value: 0.179 / Net I/σ(I): 4.1
Reflection shellResolution: 1.981→2.03 Å / Redundancy: 12.6 % / Num. unique obs: 1595 / Rsym value: 1.318 / % 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: 1.981→43.566 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.3
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.1904 3238 6.3 %
Rwork0.1616 --
obs0.1634 51379 94.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.981→43.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 38 225 3293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053171
X-RAY DIFFRACTIONf_angle_d0.8014315
X-RAY DIFFRACTIONf_dihedral_angle_d17.3881151
X-RAY DIFFRACTIONf_chiral_restr0.055440
X-RAY DIFFRACTIONf_plane_restr0.005546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9812-2.01080.2433710.2205996X-RAY DIFFRACTION40
2.0108-2.04220.274740.20991150X-RAY DIFFRACTION46
2.0422-2.07570.2384820.19861232X-RAY DIFFRACTION50
2.0757-2.11150.2091860.19591326X-RAY DIFFRACTION53
2.1115-2.14980.1918980.17611409X-RAY DIFFRACTION57
2.1498-2.19120.2328970.18171545X-RAY DIFFRACTION61
2.1912-2.23590.25741330.16921733X-RAY DIFFRACTION70
2.2359-2.28450.16751230.16571925X-RAY DIFFRACTION78
2.2845-2.33770.21431570.16562166X-RAY DIFFRACTION86
2.3377-2.39610.18241590.17032304X-RAY DIFFRACTION93
2.3961-2.46090.20341650.16812452X-RAY DIFFRACTION99
2.4609-2.53330.27741600.16922489X-RAY DIFFRACTION100
2.5333-2.61510.18221810.17232483X-RAY DIFFRACTION100
2.6151-2.70850.19151550.16812497X-RAY DIFFRACTION100
2.7085-2.8170.20531740.17342495X-RAY DIFFRACTION100
2.817-2.94510.21561600.172501X-RAY DIFFRACTION100
2.9451-3.10040.21251710.16772479X-RAY DIFFRACTION100
3.1004-3.29460.19981680.16142499X-RAY DIFFRACTION100
3.2946-3.54880.18781750.15822477X-RAY DIFFRACTION100
3.5488-3.90570.18961660.13782512X-RAY DIFFRACTION100
3.9057-4.47040.16091540.12732507X-RAY DIFFRACTION100
4.4704-5.63040.12241650.14432489X-RAY DIFFRACTION100
5.6304-43.5760.18671640.18472475X-RAY DIFFRACTION99

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