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- PDB-9fnf: The glycoside hydrolase family 71 (GH71) member AnGH71C from Aspe... -

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Basic information

Entry
Database: PDB / ID: 9fnf
TitleThe glycoside hydrolase family 71 (GH71) member AnGH71C from Aspergillus nidulans.
ComponentsGlycoside hydrolase family 71
KeywordsCARBOHYDRATE / alpha-glucan / hydrolase / mutan / nigeran
Function / homologyglucan endo-1,3-alpha-glucosidase / glucan endo-1,3-alpha-glucosidase activity / fungal-type cell wall disassembly involved in conjugation with cellular fusion / Glycoside hydrolase family 71 / Glycosyl hydrolase family 71 / mating projection actin fusion focus / carbohydrate catabolic process / extracellular region / glucan endo-1,3-alpha-glucosidase
Function and homology information
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsMazurkewich, S. / Widen, T. / Branden, G. / Larsbrink, J.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2020-03618 Sweden
CitationJournal: Commun Biol / Year: 2025
Title: Structural and biochemical basis for activity of Aspergillus nidulans alpha-1,3-glucanases from glycoside hydrolase family 71.
Authors: Mazurkewich, S. / Widen, T. / Karlsson, H. / Evenas, L. / Ramamohan, P. / Wohlert, J. / Branden, G. / Larsbrink, J.
History
DepositionJun 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 71
B: Glycoside hydrolase family 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5879
Polymers96,4222
Non-polymers1,1657
Water22,6271256
1
A: Glycoside hydrolase family 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9355
Polymers48,2111
Non-polymers7244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6534
Polymers48,2111
Non-polymers4413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.194, 84.745, 103.322
Angle α, β, γ (deg.)90.000, 130.853, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Glycoside hydrolase family 71


Mass: 48211.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: ANIA_07349 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G5EB58
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1256 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-Tris pH 5.5 with 0.2 M ammonium sulphate and 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.33→39.08 Å / Num. obs: 397430 / % possible obs: 99.55 % / Redundancy: 3.3 % / Biso Wilson estimate: 12.51 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.08722 / Net I/σ(I): 7.62
Reflection shellResolution: 1.33→1.35 Å / Redundancy: 2.5 % / Rmerge(I) obs: 1.014 / Mean I/σ(I) obs: 0.85 / Num. unique obs: 11634 / CC1/2: 0.314 / CC star: 0.692 / % possible all: 89.33

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→39.08 Å / SU ML: 0.1361 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.7654
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1763 15265 7.5 %
Rwork0.1588 188254 -
obs0.1601 203519 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.07 Å2
Refinement stepCycle: LAST / Resolution: 1.33→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6322 0 76 1256 7654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00756942
X-RAY DIFFRACTIONf_angle_d0.95519524
X-RAY DIFFRACTIONf_chiral_restr0.0929974
X-RAY DIFFRACTIONf_plane_restr0.00741248
X-RAY DIFFRACTIONf_dihedral_angle_d13.67552462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.350.29914540.29155706X-RAY DIFFRACTION89.33
1.35-1.360.29395160.28396107X-RAY DIFFRACTION98.51
1.36-1.380.27335100.26436294X-RAY DIFFRACTION99.99
1.38-1.40.26335070.24776249X-RAY DIFFRACTION99.99
1.4-1.410.25645000.23996367X-RAY DIFFRACTION99.99
1.41-1.430.25385210.22866256X-RAY DIFFRACTION99.99
1.43-1.450.24515080.23216259X-RAY DIFFRACTION100
1.45-1.480.23915010.21666252X-RAY DIFFRACTION99.96
1.48-1.50.2255120.21066292X-RAY DIFFRACTION99.99
1.5-1.520.21325190.20436290X-RAY DIFFRACTION99.97
1.52-1.550.23114980.19876292X-RAY DIFFRACTION100
1.55-1.580.20875240.18516270X-RAY DIFFRACTION100
1.58-1.610.19364860.17496292X-RAY DIFFRACTION99.99
1.61-1.640.18015220.16646282X-RAY DIFFRACTION99.97
1.64-1.680.19055010.16036312X-RAY DIFFRACTION100
1.68-1.720.18025200.16026308X-RAY DIFFRACTION99.96
1.72-1.760.18765070.16166239X-RAY DIFFRACTION100
1.76-1.810.17515130.166324X-RAY DIFFRACTION99.93
1.81-1.860.18295070.15626264X-RAY DIFFRACTION99.96
1.86-1.920.17535060.1536307X-RAY DIFFRACTION99.99
1.92-1.990.16525120.15376283X-RAY DIFFRACTION99.99
1.99-2.070.1635120.14696332X-RAY DIFFRACTION99.94
2.07-2.160.15985110.14856307X-RAY DIFFRACTION99.97
2.16-2.270.16315060.15056296X-RAY DIFFRACTION100
2.28-2.420.16955130.14886290X-RAY DIFFRACTION99.99
2.42-2.60.17115090.15076337X-RAY DIFFRACTION100
2.6-2.870.18655200.15736353X-RAY DIFFRACTION100
2.87-3.280.1595150.14466311X-RAY DIFFRACTION99.93
3.28-4.130.13955110.12456340X-RAY DIFFRACTION99.75
4.13-39.080.14155240.12836443X-RAY DIFFRACTION99.63

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