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

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Basic information

Entry
Database: PDB / ID: 6jav
TitleCrystal structure of Ostrinia furnacalis Group II chitinase catalytic domain 1 in complex with a piperidine-thienopyridine derivative
ComponentsGroup II chitinase
KeywordsHYDROLASE / inhibitor complex / chitinase
Function / homology
Function and homology information


chitinase / chitinase activity / 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 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-BC0 / Group II chitinase
Similarity search - Component
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.437 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

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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)45,1053
Polymers44,4681
Non-polymers6362
Water6,539363
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint3 kcal/mol
Surface area14460 Å2
Unit cell
Length a, b, c (Å)98.643, 98.643, 94.884
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-BC0 / 2-{[(4-chlorophenyl)methyl]sulfanyl}-7-methyl-N-(prop-2-en-1-yl)-7,8-dihydropyrido[4',3':4,5]thieno[2,3-d]pyrimidin-4-amine


Mass: 414.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19ClN4S2 / 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.: 363 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
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: Oct 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.437→50 Å / Num. obs: 139584 / % possible obs: 100 % / Redundancy: 16.5 % / Rsym value: 0.103 / Net I/σ(I): 5.6
Reflection shellResolution: 1.437→1.46 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 2.37 / Num. unique obs: 4208 / Rsym value: 1.626 / % 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: 1.437→27.359 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.14
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.1776 3236 2.32 %
Rwork0.1613 --
obs0.1616 139584 94.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.437→27.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 41 363 3434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013179
X-RAY DIFFRACTIONf_angle_d1.1094326
X-RAY DIFFRACTIONf_dihedral_angle_d17.4031160
X-RAY DIFFRACTIONf_chiral_restr0.094439
X-RAY DIFFRACTIONf_plane_restr0.007549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4368-1.45820.254710.25693052X-RAY DIFFRACTION44
1.4582-1.4810.2639850.23733471X-RAY DIFFRACTION50
1.481-1.50530.2535840.22023497X-RAY DIFFRACTION51
1.5053-1.53120.2283880.2073646X-RAY DIFFRACTION52
1.5312-1.55910.2202910.19473739X-RAY DIFFRACTION54
1.5591-1.58910.18841040.18424146X-RAY DIFFRACTION60
1.5891-1.62150.17511210.18755012X-RAY DIFFRACTION72
1.6215-1.65680.17431470.18066108X-RAY DIFFRACTION89
1.6568-1.69530.25821570.18556789X-RAY DIFFRACTION98
1.6953-1.73770.1871620.17436877X-RAY DIFFRACTION100
1.7377-1.78470.18161660.17036926X-RAY DIFFRACTION100
1.7847-1.83720.16341610.16586920X-RAY DIFFRACTION100
1.8372-1.89640.17361820.16546911X-RAY DIFFRACTION100
1.8964-1.96420.17591500.16166947X-RAY DIFFRACTION100
1.9642-2.04280.17761760.15966903X-RAY DIFFRACTION100
2.0428-2.13580.17661660.15976903X-RAY DIFFRACTION100
2.1358-2.24830.1781730.15356956X-RAY DIFFRACTION100
2.2483-2.38910.16821610.15856876X-RAY DIFFRACTION100
2.3891-2.57340.18651520.166960X-RAY DIFFRACTION100
2.5734-2.83220.17391700.16456894X-RAY DIFFRACTION100
2.8322-3.24140.19071600.15926951X-RAY DIFFRACTION100
3.2414-4.08170.15881530.14436920X-RAY DIFFRACTION100
4.0817-27.36360.15821560.14756944X-RAY DIFFRACTION100

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