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- PDB-7vrg: Crystal structure of chitinase-h from O. furnacalis in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7vrg
TitleCrystal structure of chitinase-h from O. furnacalis in complex with Lynamicin B
ComponentsChitinase
KeywordsHYDROLASE / chitinase h / O. furnacalis / Lynamicin B
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process / extracellular region
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 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 ...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 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-7U8 / Chitinase
Similarity search - Component
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLu, Q. / Liu, T. / Zhou, Y. / Yang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Lynamicin B is a Potential Pesticide by Acting as a Lepidoptera-Exclusive Chitinase Inhibitor.
Authors: Lu, Q. / Xu, L. / Liu, L. / Zhou, Y. / Liu, T. / Song, Y. / Ju, J. / Yang, Q.
History
DepositionOct 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,1838
Polymers119,9752
Non-polymers2,2096
Water7,782432
1
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0924
Polymers59,9871
Non-polymers1,1043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0924
Polymers59,9871
Non-polymers1,1043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.908, 77.859, 81.972
Angle α, β, γ (deg.)113.634, 109.902, 95.000
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 14 - 552 / Label seq-ID: 1 - 539

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'A'AA
22chain 'B'BB

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Components

#1: Protein Chitinase


Mass: 59987.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Gene: OfChi-h / Production host: Komagataella phaffii CBS 7435 (fungus) / References: UniProt: Q4AE59
#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.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-7U8 / methyl 4-[5,6-bis(chloranyl)-1H-indol-3-yl]-3-(5-chloranyl-1H-indol-3-yl)-1H-pyrrole-2-carboxylate / Lynamicin B


Mass: 458.724 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C22H14Cl3N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: 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 natural source / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.14 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100mM HEPES pH 7.0, 26% (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: BL19U1 / Wavelength: 0.97852 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.4→43.034 Å / Num. obs: 108457 / % possible obs: 94.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 31.32 Å2 / CC1/2: 0.978 / Rsym value: 0.149 / Net I/σ(I): 4.64
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 0.88 / Num. unique obs: 7985 / CC1/2: 0.382 / Rsym value: 0.91 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5gqb

5gqb


Resolution: 2.4→43.03 Å / SU ML: 0.3129 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.2137
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2433 3880 3.58 %
Rwork0.2342 104523 -
obs0.2345 108403 95.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.98 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8472 0 144 432 9048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00838860
X-RAY DIFFRACTIONf_angle_d0.936512026
X-RAY DIFFRACTIONf_chiral_restr0.06161244
X-RAY DIFFRACTIONf_plane_restr0.01061552
X-RAY DIFFRACTIONf_dihedral_angle_d18.25893170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.31891400.32983722X-RAY DIFFRACTION93.92
2.43-2.460.36861330.33173671X-RAY DIFFRACTION94.67
2.46-2.490.38191380.32173713X-RAY DIFFRACTION95.13
2.49-2.530.34141400.30823825X-RAY DIFFRACTION95.36
2.53-2.560.30661370.30363705X-RAY DIFFRACTION94.96
2.56-2.60.32521370.29923733X-RAY DIFFRACTION94.67
2.6-2.640.31081410.29463721X-RAY DIFFRACTION94.56
2.64-2.680.29251350.29323645X-RAY DIFFRACTION94.08
2.68-2.730.34731430.29313851X-RAY DIFFRACTION95.83
2.73-2.780.27951410.28733714X-RAY DIFFRACTION95.71
2.78-2.830.26761370.2863786X-RAY DIFFRACTION95.78
2.83-2.890.30461400.28433715X-RAY DIFFRACTION95.75
2.89-2.950.32711400.27863797X-RAY DIFFRACTION95.88
2.96-3.020.29351380.26013688X-RAY DIFFRACTION94.99
3.02-3.10.23651420.25513765X-RAY DIFFRACTION95.67
3.1-3.180.2431390.24773721X-RAY DIFFRACTION95.45
3.18-3.280.25281410.24613838X-RAY DIFFRACTION95.51
3.28-3.380.22351390.22813755X-RAY DIFFRACTION95.68
3.38-3.50.20751370.2193729X-RAY DIFFRACTION95.22
3.5-3.640.27411350.2033687X-RAY DIFFRACTION94.98
3.64-3.810.20791410.20113758X-RAY DIFFRACTION95.24
3.81-4.010.16521380.19453745X-RAY DIFFRACTION95.26
4.01-4.260.21221390.17873701X-RAY DIFFRACTION95.1
4.26-4.590.1821410.18473794X-RAY DIFFRACTION94.91
4.59-5.050.18751380.18563666X-RAY DIFFRACTION94.53
5.05-5.780.25361400.20623714X-RAY DIFFRACTION94.05
5.78-7.270.21271330.22313697X-RAY DIFFRACTION94.29
7.28-43.030.19361370.21073667X-RAY DIFFRACTION93.37

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