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- PDB-6jmb: Crystal structure of Ostrinia furnacalis Group IV chitinase in co... -

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Basic information

Entry
Database: PDB / ID: 6jmb
TitleCrystal structure of Ostrinia furnacalis Group IV chitinase in complex with allosamidin
Componentsofchtiv-allosamidin
KeywordsHYDROLASE / chitinase / group IV / allosamidin
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
Allosamidin / ALLOSAMIZOLINE / Group IV chitinase
Similarity search - Component
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.389 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 2.0Apr 13, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_conn_type / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list
Revision 2.1Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ofchtiv-allosamidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5843
Polymers43,9431
Non-polymers6412
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-4 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.625, 71.707, 72.155
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-allosamidin


Mass: 43943.258 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-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: Allosamidin
DescriptorTypeProgram
DAllpNAcb1-4DAllpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2222h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-AllpNAc]{[(4+1)][b-D-AllpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-AMI / ALLOSAMIZOLINE


Type: Oligosaccharide / Class: Inhibitor / Mass: 216.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N2O4 / References: Allosamidin
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 1.96 Å3/Da / Density % sol: 37.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20%(v/v) 1,4-butanediol, 100mM sodium acetate, 100mM acetic acid, pH 4.5

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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 315r / 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: 1.389→50 Å / Num. obs: 124774 / % possible obs: 100 % / Redundancy: 8.5 % / Rsym value: 0.058 / Net I/σ(I): 9.7
Reflection shellResolution: 1.39→1.41 Å / Redundancy: 8.2 % / Num. unique obs: 5609 / Rsym value: 0.372 / % possible all: 100

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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: 1.389→25.431 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.2
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.1595 3493 2.8 %
Rwork0.1494 --
obs0.1497 124774 92.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.389→25.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 43 285 3265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053081
X-RAY DIFFRACTIONf_angle_d0.8544215
X-RAY DIFFRACTIONf_dihedral_angle_d15.7611070
X-RAY DIFFRACTIONf_chiral_restr0.081463
X-RAY DIFFRACTIONf_plane_restr0.005547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3889-1.40790.1787960.17892658X-RAY DIFFRACTION51
1.4079-1.4280.2019860.17383162X-RAY DIFFRACTION60
1.428-1.44940.19331010.16663564X-RAY DIFFRACTION68
1.4494-1.4720.1839850.16013962X-RAY DIFFRACTION75
1.472-1.49610.20951060.15854382X-RAY DIFFRACTION83
1.4961-1.52190.17341510.15694635X-RAY DIFFRACTION89
1.5219-1.54960.19361310.15734967X-RAY DIFFRACTION94
1.5496-1.57940.18791740.15415025X-RAY DIFFRACTION96
1.5794-1.61160.15991350.15125189X-RAY DIFFRACTION99
1.6116-1.64670.18591550.15315225X-RAY DIFFRACTION100
1.6467-1.6850.15681570.1515198X-RAY DIFFRACTION100
1.685-1.72710.14421340.1485263X-RAY DIFFRACTION100
1.7271-1.77380.16851380.14455217X-RAY DIFFRACTION100
1.7738-1.8260.15451820.14135215X-RAY DIFFRACTION100
1.826-1.88490.14581440.14445279X-RAY DIFFRACTION100
1.8849-1.95220.13971780.14615208X-RAY DIFFRACTION100
1.9522-2.03030.14961320.14355244X-RAY DIFFRACTION100
2.0303-2.12270.13551540.14375259X-RAY DIFFRACTION100
2.1227-2.23460.1451420.14665227X-RAY DIFFRACTION100
2.2346-2.37450.15881460.15255237X-RAY DIFFRACTION100
2.3745-2.55760.17191640.14865226X-RAY DIFFRACTION100
2.5576-2.81470.16151660.15985217X-RAY DIFFRACTION100
2.8147-3.22130.17871320.15395250X-RAY DIFFRACTION100
3.2213-4.05590.15161470.14765243X-RAY DIFFRACTION100
4.0559-25.43530.15311570.1425229X-RAY DIFFRACTION100

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