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- PDB-7bly: Structure of the chitin deacetylase AngCDA from Aspergillus niger -

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Basic information

Entry
Database: PDB / ID: 7bly
TitleStructure of the chitin deacetylase AngCDA from Aspergillus niger
ComponentsAspergillus niger contig An12c0130, genomic contig
KeywordsHYDROLASE / chitin deacetylase chitosan Aspergillus niger
Function / homologychitin deacetylase / chitin deacetylase activity / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / carbohydrate metabolic process / MALONATE ION / Aspergillus niger contig An12c0130, genomic contig
Function and homology information
Biological speciesAspergillus niger CBS 513.88 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsRoret, T. / Bonin, M. / Hembach, L. / Moerschbacher, B.M.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: In silico and in vitro analysis of an Aspergillus niger chitin deacetylase to decipher its subsite sugar preferences.
Authors: Bonin, M. / Hameleers, L. / Hembach, L. / Roret, T. / Cord-Landwehr, S. / Michel, G. / Moerschbacher, B.M.
History
DepositionJan 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 13, 2021Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspergillus niger contig An12c0130, genomic contig
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5814
Polymers26,3791
Non-polymers2033
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-42 kcal/mol
Surface area8950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.874, 119.874, 119.874
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number207
Space group name H-MP432
Space group name HallP423
Symmetry operation#1: x,y,z
#2: x,-z,y
#3: x,z,-y
#4: z,y,-x
#5: -z,y,x
#6: -y,x,z
#7: y,-x,z
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y,x,-z
#20: -y,-x,-z
#21: z,-y,x
#22: -z,-y,-x
#23: -x,z,y
#24: -x,-z,-y
Components on special symmetry positions
IDModelComponents
11A-543-

HOH

21A-623-

HOH

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Components

#1: Protein Aspergillus niger contig An12c0130, genomic contig


Mass: 26378.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger CBS 513.88 (mold) / Gene: An12g04480 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2QZC8, chitin deacetylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.4 M sodium malonate 0.1 M Bis-Tris propane pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980116 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980116 Å / Relative weight: 1
ReflectionResolution: 1.81→48.94 Å / Num. obs: 27485 / % possible obs: 100 % / Redundancy: 77.5 % / CC1/2: 0.999 / Rpim(I) all: 0.043 / Net I/σ(I): 18.6
Reflection shellResolution: 1.81→1.85 Å / Redundancy: 79.66 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1613 / CC1/2: 0.716 / Rpim(I) all: 0.771 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
Coot0.8.9.2model building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y8U

2y8u


Resolution: 1.81→42.38 Å / SU ML: 0.1542 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.7975
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1855 1357 4.94 %
Rwork0.1526 26127 -
obs0.1542 27484 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.56 Å2
Refinement stepCycle: LAST / Resolution: 1.81→42.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 9 230 1927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631771
X-RAY DIFFRACTIONf_angle_d0.88912422
X-RAY DIFFRACTIONf_chiral_restr0.0522281
X-RAY DIFFRACTIONf_plane_restr0.0058320
X-RAY DIFFRACTIONf_dihedral_angle_d18.3274652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.870.25141400.2212556X-RAY DIFFRACTION100
1.87-1.950.24311380.18752534X-RAY DIFFRACTION100
1.95-2.040.20481240.16552586X-RAY DIFFRACTION100
2.04-2.150.18161520.15672545X-RAY DIFFRACTION100
2.15-2.280.19421390.15222545X-RAY DIFFRACTION100
2.28-2.460.231220.17222600X-RAY DIFFRACTION100
2.46-2.70.18471560.16612583X-RAY DIFFRACTION100
2.7-3.090.21691330.16852625X-RAY DIFFRACTION100
3.1-3.90.16741050.13122699X-RAY DIFFRACTION100
3.9-42.380.14651480.1332854X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 27.4440831873 Å / Origin y: 46.9700749366 Å / Origin z: -15.7570582655 Å
111213212223313233
T0.172169925973 Å20.0187916856149 Å20.0044218662078 Å2-0.136480413718 Å2-0.0138189512141 Å2--0.146449550306 Å2
L0.512467387346 °2-0.123924672835 °20.197502561895 °2-1.01471786771 °20.0805594146028 °2--1.3723489156 °2
S0.0525854501731 Å °0.0452713014239 Å °-0.00463294428249 Å °0.0489537371205 Å °0.0137212508676 Å °0.00864913990354 Å °0.121752298344 Å °0.0890830476979 Å °0.00152512923287 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 24 through 239)

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