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- PDB-6jm8: Crystal structure of Ostrinia furnacalis Group IV chitinase -

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Basic information

Entry
Database: PDB / ID: 6jm8
TitleCrystal structure of Ostrinia furnacalis Group IV chitinase
Componentsofchtiv-g5
KeywordsHYDROLASE / chitinase / Ostrinia furnacalis / group IV
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
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: 1.911 Å
AuthorsLiu, T. / Yang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31425021 China
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2020
Title: Structure and property of group IV insect chitinase, a potential drug target and biopesticide
Authors: Liu, T. / Guo, X. / Bu, Y. / Zhou, Y. / Duan, Y. / Yang, Q.
History
DepositionMar 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.year
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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 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

Downloads & links

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Assembly

Deposited unit
A: ofchtiv-g5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9612
Polymers43,9271
Non-polymers1,0341
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint25 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.573, 73.781, 89.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ofchtiv-g5


Mass: 43927.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Plasmid: pPic9k / Production host: Pichia (fungus) / Strain (production host): GS115 / References: UniProt: A0A482LWB1*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1033.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 1600 mM sodium phosphate monobasic, 400 mM potassium phosphate dibasic, 100 mM sodium phosphate dibasic, 100 mM citric acid, pH 4.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97778 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97778 Å / Relative weight: 1
ReflectionResolution: 1.911→50 Å / Num. obs: 43869 / % possible obs: 99.7 % / Redundancy: 7.8 % / Rsym value: 0.214 / Net I/σ(I): 4.8
Reflection shellResolution: 1.911→1.95 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 3.87 / Num. unique obs: 3321 / Rsym value: 1.355 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5wup

5wup


Resolution: 1.911→31.679 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.3
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.1986 3156 7.24 %
Rwork0.1768 --
obs0.1784 43619 77.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.911→31.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2919 0 71 210 3200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043073
X-RAY DIFFRACTIONf_angle_d0.7164204
X-RAY DIFFRACTIONf_dihedral_angle_d17.3981083
X-RAY DIFFRACTIONf_chiral_restr0.059469
X-RAY DIFFRACTIONf_plane_restr0.005540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9113-1.93980.5653450.5339560X-RAY DIFFRACTION24
1.9398-1.97010.2629800.27511017X-RAY DIFFRACTION46
1.9701-2.00240.2329890.20841146X-RAY DIFFRACTION50
2.0024-2.0370.2534920.20051188X-RAY DIFFRACTION53
2.037-2.0740.2399960.21921236X-RAY DIFFRACTION55
2.074-2.11390.21211030.20631332X-RAY DIFFRACTION58
2.1139-2.1570.1971010.19111377X-RAY DIFFRACTION61
2.157-2.20390.18571160.18531463X-RAY DIFFRACTION65
2.2039-2.25520.3707880.29541095X-RAY DIFFRACTION48
2.2552-2.31150.24221360.21121636X-RAY DIFFRACTION73
2.3115-2.3740.21351500.1791931X-RAY DIFFRACTION85
2.374-2.44390.22631540.17142060X-RAY DIFFRACTION91
2.4439-2.52270.21961710.17922147X-RAY DIFFRACTION95
2.5227-2.61280.24621670.18392187X-RAY DIFFRACTION98
2.6128-2.71740.21451760.18432231X-RAY DIFFRACTION99
2.7174-2.8410.2041640.1852220X-RAY DIFFRACTION98
2.841-2.99070.22771760.1832250X-RAY DIFFRACTION99
2.9907-3.17790.21031720.18862229X-RAY DIFFRACTION100
3.1779-3.4230.19561780.17082256X-RAY DIFFRACTION100
3.423-3.76690.16861740.16952208X-RAY DIFFRACTION98
3.7669-4.31090.13871740.14172219X-RAY DIFFRACTION98
4.3109-5.42680.15271720.13382245X-RAY DIFFRACTION100
5.4268-31.6830.18561820.17112230X-RAY DIFFRACTION99

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