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- PDB-5zns: Insect chitin deacetylase -

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Basic information

Entry
Database: PDB / ID: 5zns
TitleInsect chitin deacetylase
Componentschitin deacetylase
KeywordsHYDROLASE / Chitin deacetylase / Bombyx mori / activity / chitin binding / chitosan
Function / homology
Function and homology information


chitin deacetylase / chitin deacetylase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular space / zinc ion binding
Similarity search - Function
NodB homology domain / Polysaccharide deacetylase / Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site ...NodB homology domain / Polysaccharide deacetylase / Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily
Similarity search - Domain/homology
Chitin deacetylase 1
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.396 Å
AuthorsLiu, L. / Zhou, Y. / Yang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31772193 China
Citation
Journal: J. Biol. Chem. / Year: 2019
Title: Structural and biochemical insights into the catalytic mechanisms of two insect chitin deacetylases of the carbohydrate esterase 4 family.
Authors: Liu, L. / Zhou, Y. / Qu, M. / Qiu, Y. / Guo, X. / Zhang, Y. / Liu, T. / Yang, J. / Yang, Q.
#1: Journal: INSECT MOL.BIOL. / Year: 2017
Title: The physiological differentiation along the midgut of Bombyx mori-inspirations from the proteomics and gene expression patterns of the secreted proteins in the ectoperitrophic space
Authors: Liu, L. / Qu, M. / Yang, J. / Yang, Q.
History
DepositionApr 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 24, 2019Group: Data collection / 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: chitin deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7574
Polymers45,0461
Non-polymers7113
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-24 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.941, 134.941, 77.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-931-

HOH

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Components

#1: Protein chitin deacetylase /


Mass: 45046.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: LOC101740647 / Production host: Komagataella pastoris GS115 (fungus) / References: UniProt: H9J9M0
#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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated 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
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 3.94 Å3/Da / Density % sol: 68.8 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium malonate pH 7.0, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979452 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979452 Å / Relative weight: 1
ReflectionResolution: 2.396→50 Å / Num. obs: 27348 / % possible obs: 100 % / Redundancy: 14.7 % / Rsym value: 0.057 / Net I/σ(I): 17.9
Reflection shellResolution: 2.396→2.44 Å / Num. unique obs: 1364 / Rsym value: 0.156

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.396→47.526 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.75
RfactorNum. reflection% reflection
Rfree0.1899 2001 7.33 %
Rwork0.1628 --
obs0.1647 27310 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.396→47.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3090 0 43 233 3366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013244
X-RAY DIFFRACTIONf_angle_d1.0324436
X-RAY DIFFRACTIONf_dihedral_angle_d16.9531201
X-RAY DIFFRACTIONf_chiral_restr0.084466
X-RAY DIFFRACTIONf_plane_restr0.006585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3957-2.45560.22751400.17981785X-RAY DIFFRACTION98
2.4556-2.5220.2481390.17841767X-RAY DIFFRACTION100
2.522-2.59620.21891420.18371800X-RAY DIFFRACTION100
2.5962-2.680.22391440.19651808X-RAY DIFFRACTION100
2.68-2.77580.23581430.18881798X-RAY DIFFRACTION100
2.7758-2.88690.20821410.18091810X-RAY DIFFRACTION100
2.8869-3.01830.20071380.17961792X-RAY DIFFRACTION100
3.0183-3.17740.20181350.18361806X-RAY DIFFRACTION100
3.1774-3.37640.20761430.17291818X-RAY DIFFRACTION100
3.3764-3.6370.19981500.15771801X-RAY DIFFRACTION100
3.637-4.00290.18341440.14621813X-RAY DIFFRACTION100
4.0029-4.58170.15221450.12721825X-RAY DIFFRACTION100
4.5817-5.77090.15621460.1411831X-RAY DIFFRACTION100
5.7709-47.53540.17171510.1721855X-RAY DIFFRACTION100

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