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- PDB-5y2a: Crystal structure of Ostrinia furnacalis Group II chitinase catal... -

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Basic information

Entry
Database: PDB / ID: 5y2a
TitleCrystal structure of Ostrinia furnacalis Group II chitinase catalytic domain 2
Componentsinsect group II chitinase
KeywordsHYDROLASE / GH18 chitinase
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 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily / Chitinase II ...Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / 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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChen, W. / Qu, M.B. / Zhou, Y. / Yang, Q.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural analysis of group II chitinase (ChtII) catalysis completes the puzzle of chitin hydrolysis in insects
Authors: Chen, W. / Qu, M. / Zhou, Y. / Yang, Q.
History
DepositionJul 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _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 / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 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: insect group II chitinase
B: insect group II chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0884
Polymers86,9422
Non-polymers2,1462
Water12,322684
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint34 kcal/mol
Surface area30100 Å2
Unit cell
Length a, b, c (Å)72.637, 90.654, 74.856
Angle α, β, γ (deg.)90.000, 116.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein insect group II chitinase


Mass: 43471.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Production host: Komagataella pastoris GS115 (fungus) / References: UniProt: A0A221ZS22*PLUS, chitinase
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2/a4-b1_b4-c1_c3-d1_d2-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium acetate, 0.1M Bis-Tris, 45% 2-methyl-2,4-pentadiol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 68407 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.055 / Rrim(I) all: 0.145 / Χ2: 1.004 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.935.80.48666140.9020.2160.5331.01799.9
1.93-1.975.90.4590.9080.2030.5030.992100
1.97-2.015.90.410.9220.180.4491.00499.9
2.01-2.055.90.3810.9360.1690.4181.00999.9
2.05-2.096.30.350.9430.1490.3811.033100
2.09-2.146.80.3280.9560.1350.3551.027100
2.14-2.196.90.3030.960.1230.3271.045100
2.19-2.2570.2750.9680.1120.2971.03399.9
2.25-2.326.90.2530.9720.1040.2731.038100
2.32-2.396.70.2220.9770.0920.2411.00699.9
2.39-2.486.40.2060.980.0880.2251.023100
2.48-2.586.80.1920.9810.0790.2081.047100
2.58-2.77.10.1760.9840.0710.191.04399.9
2.7-2.8470.1530.9870.0620.1651.03399.9
2.84-3.026.90.1330.9890.0540.1441.0399.8
3.02-3.256.50.110.9910.0470.12199.9
3.25-3.587.10.0980.9930.0390.1051.00599.9
3.58-4.097.10.0850.9940.0340.0910.96699.9
4.09-5.166.60.0780.9940.0330.0850.90399.9
5.16-506.90.0770.9950.0310.0830.836100

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Processing

Software
NameVersionClassification
PHENIX1.11_2567refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
Cootmodel building
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GUV

1guv


Resolution: 1.9→50 Å / Cross valid method: NONE
RfactorNum. reflection% reflection
Rfree0.1859 1958 -
Rwork0.1665 --
obs-68407 100 %
Displacement parametersBiso max: 83.23 Å2 / Biso mean: 22.2633 Å2 / Biso min: 9.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6132 0 144 684 6960
LS refinement shellResolution: 1.8994→1.9469 Å
RfactorNum. reflection% reflection
Rfree0.2549 128 -
Rwork0.2266 4532 -
obs--96 %

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