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- PDB-3wl0: Crystal structure of Ostrinia furnacalis Group I chitinase cataly... -

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Basic information

Entry
Database: PDB / ID: 3wl0
TitleCrystal structure of Ostrinia furnacalis Group I chitinase catalytic domain E148A mutant in complex with a(GlcNAc)2
ComponentsChitinase
KeywordsHYDROLASE / glycosyl hydrolase / insect / Ostrinia furnacalis
Function / homology
Function and homology information


endochitinase activity / chitinase / 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 / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily ...Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Chitinase A; domain 3 - #10 / 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. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å
AuthorsChen, L. / Liu, T. / Zhou, Y. / Chen, Q. / Shen, X. / Yang, Q.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural characteristics of an insect group I chitinase, an enzyme indispensable to moulting.
Authors: Chen, L. / Liu, T. / Zhou, Y. / Chen, Q. / Shen, X. / Yang, Q.
History
DepositionNov 5, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / 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 / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)45,8044
Polymers44,9381
Non-polymers8673
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.113, 94.113, 122.312
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Chitinase


Mass: 44937.578 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 19-407 / Mutation: E148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Production host: Komagataella pastoris (fungus) / References: UniProt: Q2V6H4, 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-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
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#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.: 342 / Source method: isolated from a natural source / Formula: H2O
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: 3.48 Å3/Da / Density % sol: 64.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 100mM HEPES pH 7.9, 23% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 31026 / Num. obs: 31013 / % possible obs: 99.89 % / Redundancy: 16.9 % / Biso Wilson estimate: 23.51 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 24.81
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 17 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 12.32 / Rsym value: 0.368 / % possible all: 98.93

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W4R

3w4r


Resolution: 2.204→38.663 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1796 1992 6.43 %
Rwork0.1511 --
obs0.1529 30957 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.204→38.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3071 0 57 342 3470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063233
X-RAY DIFFRACTIONf_angle_d1.0424394
X-RAY DIFFRACTIONf_dihedral_angle_d14.9631178
X-RAY DIFFRACTIONf_chiral_restr0.075455
X-RAY DIFFRACTIONf_plane_restr0.004558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2036-2.25870.19341400.1612022X-RAY DIFFRACTION98
2.2587-2.31980.19971410.16262052X-RAY DIFFRACTION100
2.3198-2.3880.21581420.16452068X-RAY DIFFRACTION100
2.388-2.46510.21821430.1712056X-RAY DIFFRACTION100
2.4651-2.55320.21421460.16542075X-RAY DIFFRACTION100
2.5532-2.65540.18851430.16782069X-RAY DIFFRACTION100
2.6554-2.77620.21071460.16572071X-RAY DIFFRACTION100
2.7762-2.92250.1811430.1582056X-RAY DIFFRACTION100
2.9225-3.10550.19681380.16192065X-RAY DIFFRACTION100
3.1055-3.34520.17311500.15792088X-RAY DIFFRACTION100
3.3452-3.68160.17041380.13712072X-RAY DIFFRACTION100
3.6816-4.21380.15631390.12792068X-RAY DIFFRACTION100
4.2138-5.30670.13581420.12472099X-RAY DIFFRACTION100
5.3067-38.66860.19051410.16842104X-RAY DIFFRACTION100

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