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

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Basic information

Entry
Database: PDB / ID: 6jax
TitleCrystal structure of Ostrinia furnacalis Group II chitinase catalytic domain 1 in complex with chitooctaose [(GlcN)8]
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 / Glyco_18 ...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. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)46,2003
Polymers44,4681
Non-polymers1,7322
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint24 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.600, 98.600, 94.993
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: 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: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2- ...2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1307.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNb1-4DGlcpNb1-4DGlcpNb1-4DGlcpNb1-4DGlcpNb1-4DGlcpNb1-4DGlcpNb1-4DGlcpNb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,8,7/[a2122h-1b_1-5_2*N]/1-1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{}}}}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 52.62 %
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: 0.97776 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 52050 / % possible obs: 100 % / Redundancy: 25.4 % / Rsym value: 0.195 / Net I/σ(I): 3.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 24.8 % / Mean I/σ(I) obs: 3.83 / Num. unique obs: 2538 / Rsym value: 0.665 / % 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: 1.7→44.095 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.66
RfactorNum. reflection% reflection
Rfree0.1791 2015 3.88 %
Rwork0.1517 --
obs0.1528 51967 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→44.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 117 464 3611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013284
X-RAY DIFFRACTIONf_angle_d1.2164485
X-RAY DIFFRACTIONf_dihedral_angle_d14.6391160
X-RAY DIFFRACTIONf_chiral_restr0.068486
X-RAY DIFFRACTIONf_plane_restr0.006554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7002-1.74270.19751330.16263490X-RAY DIFFRACTION100
1.7427-1.78980.19531510.15833506X-RAY DIFFRACTION100
1.7898-1.84250.18951360.15783505X-RAY DIFFRACTION100
1.8425-1.90190.19851350.15443559X-RAY DIFFRACTION100
1.9019-1.96990.20711440.14923505X-RAY DIFFRACTION100
1.9699-2.04880.20621410.15233537X-RAY DIFFRACTION100
2.0488-2.1420.15671500.15223544X-RAY DIFFRACTION100
2.142-2.2550.16851330.14883533X-RAY DIFFRACTION100
2.255-2.39620.18721510.15223541X-RAY DIFFRACTION100
2.3962-2.58120.1741410.15353583X-RAY DIFFRACTION100
2.5812-2.84090.18431470.15483566X-RAY DIFFRACTION100
2.8409-3.25190.15341430.15173606X-RAY DIFFRACTION100
3.2519-4.09660.14591480.14143662X-RAY DIFFRACTION100
4.0966-44.11010.2091620.15593815X-RAY DIFFRACTION100

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