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- PDB-6igy: Crystal structure of Aspergillus niger chitinase B -

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Basic information

Entry
Database: PDB / ID: 6igy
TitleCrystal structure of Aspergillus niger chitinase B
ComponentsGlycosyl hydrolases family 18 family protein
KeywordsHYDROLASE / Ostrinia furnacalis / chitinase / three-dimensional structure / chitin metabolism / (GlcNAc)5
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process
Similarity search - Function
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. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 ...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. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.948 Å
AuthorsLiu, T. / Zhou, Y. / Yang, Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31425021 China
National Natural Science Foundation of China61202252 China
CitationJournal: J.Agric.Food Chem. / Year: 2020
Title: Potent Fungal Chitinase for the Bioconversion of Mycelial Waste.
Authors: Liu, T. / Han, H. / Wang, D. / Guo, X. / Zhou, Y. / Fukamizo, T. / Yang, Q.
History
DepositionSep 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 20, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl hydrolases family 18 family protein


Theoretical massNumber of molelcules
Total (without water)45,2931
Polymers45,2931
Non-polymers00
Water6,251347
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15530 Å2
Unit cell
Length a, b, c (Å)62.095, 74.956, 99.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycosyl hydrolases family 18 family protein / chitinase B


Mass: 45293.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Strain: CBS 513.88 / FGSC A1513 / Gene: An08g09030 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A5AB48, chitinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES sodium, 800 mM potassium sodium tartrate tetrahydrate.
PH range: 7.1-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97775 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 1.948→50 Å / Num. obs: 34419 / % possible obs: 99.8 % / Redundancy: 11.3 % / Rsym value: 0.19 / Net I/σ(I): 5.3
Reflection shellResolution: 1.948→1.98 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WNO

1wno


Resolution: 1.948→47.818 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.35
RfactorNum. reflection% reflection
Rfree0.1958 1913 5.99 %
Rwork0.1694 --
obs0.171 31939 92.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.948→47.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3041 0 0 347 3388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043135
X-RAY DIFFRACTIONf_angle_d0.614268
X-RAY DIFFRACTIONf_dihedral_angle_d16.7261112
X-RAY DIFFRACTIONf_chiral_restr0.043450
X-RAY DIFFRACTIONf_plane_restr0.004555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9484-1.99720.2464930.19491524X-RAY DIFFRACTION67
1.9972-2.05120.21761110.19211719X-RAY DIFFRACTION76
2.0512-2.11150.2211220.18561962X-RAY DIFFRACTION85
2.1115-2.17970.20821350.17992085X-RAY DIFFRACTION92
2.1797-2.25760.2461350.17422192X-RAY DIFFRACTION95
2.2576-2.3480.20461420.17322157X-RAY DIFFRACTION94
2.348-2.45480.23751400.17792189X-RAY DIFFRACTION96
2.4548-2.58420.18771410.17562235X-RAY DIFFRACTION97
2.5842-2.74610.20041420.17792226X-RAY DIFFRACTION97
2.7461-2.95810.22031500.17032297X-RAY DIFFRACTION98
2.9581-3.25580.21081470.16722307X-RAY DIFFRACTION99
3.2558-3.72670.16041490.15562316X-RAY DIFFRACTION100
3.7267-4.69460.15741520.13992369X-RAY DIFFRACTION100
4.6946-47.83240.18961540.18682448X-RAY DIFFRACTION98

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