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- PDB-6jmn: Crystal structure of Ostrinia furnacalis Chitinase h complexed wi... -

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Basic information

Entry
Database: PDB / ID: 6jmn
TitleCrystal structure of Ostrinia furnacalis Chitinase h complexed with compound 2-8-s2
ComponentsChitinase
KeywordsHYDROLASE / chitianse / complex / Ostrinia furnacalis / inhibitor
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process
Similarity search - Function
Chitinase A N-terminal / Chitinase A, N-terminal domain / 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. ...Chitinase A N-terminal / Chitinase A, N-terminal domain / 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 / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-BV0 / Chitinase
Similarity search - Component
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJiang, X. / Yang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31425021 China
CitationJournal: J.Med.Chem. / Year: 2020
Title: A Series of Compounds Bearing a Dipyrido-Pyrimidine Scaffold Acting as Novel Human and Insect Pest Chitinase Inhibitors.
Authors: Jiang, X. / Kumar, A. / Motomura, Y. / Liu, T. / Zhou, Y. / Moro, K. / Zhang, K.Y.J. / Yang, Q.
History
DepositionMar 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 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 / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 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 1.3Oct 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: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9584
Polymers61,0701
Non-polymers8883
Water32418
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint8 kcal/mol
Surface area21000 Å2
Unit cell
Length a, b, c (Å)48.496, 108.684, 122.442
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)

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Components

#1: Protein Chitinase


Mass: 61069.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Gene: OfChi-h / Plasmid: pPIC9 / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q4AE59
#2: Chemical ChemComp-BV0 / 6-azanyl-11-methyl-2-oxidanylidene-7-[[(2R)-oxolan-2-yl]methyl]-N-(pyridin-3-ylmethyl)-1,9-diaza-7-azoniatricyclo[8.4.0.0^{3,8}]tetradeca-3(8),4,6,9,11,13-hexaene-5-carboxamide


Mass: 445.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25N6O3 / 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.: 2
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.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM HEPES pH 7.0, 30% (w/v) Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 23127 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 62.02 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.022 / Rrim(I) all: 0.078 / Χ2: 0.685 / Net I/σ(I): 6.1 / Num. measured all: 296941
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5412.70.73511630.8890.2130.7660.43399.9
2.54-2.59130.6511100.920.1860.6760.44799.9
2.59-2.6413.10.57711280.9380.1640.60.448100
2.64-2.6913.10.47211520.9590.1350.4910.456100
2.69-2.7512.80.43411150.9630.1260.4520.463100
2.75-2.8212.30.35811230.9710.1060.3740.493100
2.82-2.8912.80.31111450.9790.090.3240.526100
2.89-2.9613.60.24711380.9870.0690.2570.571100
2.96-3.0513.40.19311560.9910.0540.20.549100
3.05-3.1513.40.15811160.9940.0450.1640.558100
3.15-3.2613.10.12911560.9960.0370.1340.597100
3.26-3.3912.40.10811590.9960.0320.1120.657100
3.39-3.5512.40.08911420.9980.0260.0920.764100
3.55-3.7313.40.07511680.9980.0210.0780.817100
3.73-3.9713.30.06711500.9980.0190.0690.89100
3.97-4.27130.06111490.9980.0170.0641.041100
4.27-4.712.20.05511830.9980.0160.0581.076100
4.7-5.3813.30.05211880.9990.0150.0541.01699.9
5.38-6.7812.20.04911990.9980.0150.0510.817100
6.78-5011.40.0512870.9990.0150.0521.05999.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GPR

5gpr


Resolution: 2.5→27.17 Å / SU ML: 0.3515 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.1475 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2496 2000 8.68 %
Rwork0.2033 21032 -
obs0.2072 23032 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.81 Å2
Refinement stepCycle: LAST / Resolution: 2.5→27.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4197 0 61 18 4276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224382
X-RAY DIFFRACTIONf_angle_d0.53765951
X-RAY DIFFRACTIONf_chiral_restr0.0431613
X-RAY DIFFRACTIONf_plane_restr0.0031770
X-RAY DIFFRACTIONf_dihedral_angle_d4.81272528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.34771410.28781491X-RAY DIFFRACTION99.51
2.56-2.630.4141400.27351462X-RAY DIFFRACTION100
2.63-2.710.35151400.26751486X-RAY DIFFRACTION100
2.71-2.80.31091410.26311471X-RAY DIFFRACTION100
2.8-2.90.33261400.26931470X-RAY DIFFRACTION99.94
2.9-3.010.31261420.25751496X-RAY DIFFRACTION100
3.01-3.150.30591390.26271469X-RAY DIFFRACTION100
3.15-3.320.31941430.25911511X-RAY DIFFRACTION99.94
3.32-3.530.26241430.24011488X-RAY DIFFRACTION100
3.53-3.80.25461430.20741507X-RAY DIFFRACTION99.94
3.8-4.180.19061420.17471496X-RAY DIFFRACTION100
4.18-4.780.21281450.15491534X-RAY DIFFRACTION100
4.78-6.010.21831470.17491546X-RAY DIFFRACTION99.88
6.01-27.170.221540.17781605X-RAY DIFFRACTION98.54

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