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

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Basic information

Entry
Database: PDB / ID: 9fng
TitleThe glycoside hydrolase family 71 (GH71) member AnGH71C from Aspergillus nidulans in complex with glucose.
ComponentsGlycoside hydrolase family 71
KeywordsCARBOHYDRATE / alpha-glucan / hydrolase / mutan / nigeran
Function / homology
Function and homology information


glucan endo-1,3-alpha-glucosidase / glucan endo-1,3-alpha-glucosidase activity / fungal-type cell wall disassembly involved in conjugation with cellular fusion / mating projection actin fusion focus / carbohydrate catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase family 71 / Glycosyl hydrolase family 71
Similarity search - Domain/homology
beta-D-glucopyranose / alpha-D-glucopyranose / glucan endo-1,3-alpha-glucosidase
Similarity search - Component
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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)97,1436
Polymers96,4222
Non-polymers7214
Water18,2311012
1
A: Glycoside hydrolase family 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5713
Polymers48,2111
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5713
Polymers48,2111
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.018, 84.413, 102.224
Angle α, β, γ (deg.)90.000, 130.560, 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: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1012 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Citrate pH 5.0 with 20 % w/v PEG 6000

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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: 1.37→42.09 Å / Num. obs: 353567 / % possible obs: 98.81 % / Redundancy: 3.3 % / Biso Wilson estimate: 14.69 Å2 / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 7.52
Reflection shellResolution: 1.37→1.38 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 0.81 / Num. unique obs: 9796 / CC1/2: 0.332 / CC star: 0.706 / % possible all: 85.82

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→42.09 Å / SU ML: 0.1431 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.9602
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1821 13567 7.5 %
Rwork0.1633 167286 -
obs0.1647 180853 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.09 Å2
Refinement stepCycle: LAST / Resolution: 1.37→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6288 0 48 1012 7348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616681
X-RAY DIFFRACTIONf_angle_d0.88929158
X-RAY DIFFRACTIONf_chiral_restr0.0877966
X-RAY DIFFRACTIONf_plane_restr0.00661198
X-RAY DIFFRACTIONf_dihedral_angle_d13.64842338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.380.27933900.28024858X-RAY DIFFRACTION85.82
1.38-1.40.34440.2715427X-RAY DIFFRACTION96.77
1.4-1.420.29014340.26485527X-RAY DIFFRACTION98.46
1.42-1.440.27414730.25745550X-RAY DIFFRACTION98.58
1.44-1.450.27274450.24865507X-RAY DIFFRACTION98.69
1.45-1.470.26244430.24235623X-RAY DIFFRACTION98.67
1.47-1.50.24124630.23265464X-RAY DIFFRACTION98.82
1.5-1.520.2474470.22285558X-RAY DIFFRACTION98.77
1.52-1.540.23544380.21265608X-RAY DIFFRACTION98.89
1.54-1.570.21814610.20515562X-RAY DIFFRACTION98.9
1.57-1.590.22674540.20025589X-RAY DIFFRACTION98.98
1.59-1.620.21654630.19385567X-RAY DIFFRACTION99.21
1.62-1.650.21034450.18115605X-RAY DIFFRACTION99.31
1.65-1.690.20554610.18065566X-RAY DIFFRACTION99.29
1.69-1.720.21824430.18035611X-RAY DIFFRACTION99.18
1.72-1.760.20874650.17975586X-RAY DIFFRACTION99.46
1.76-1.810.20854450.1815614X-RAY DIFFRACTION99.57
1.81-1.860.19794600.17355572X-RAY DIFFRACTION99.46
1.86-1.910.18754610.16945637X-RAY DIFFRACTION99.67
1.91-1.970.19834620.16575587X-RAY DIFFRACTION99.57
1.97-2.040.19034430.16145661X-RAY DIFFRACTION99.69
2.04-2.130.17244540.15885594X-RAY DIFFRACTION99.75
2.13-2.220.18894610.16195674X-RAY DIFFRACTION99.8
2.22-2.340.17444540.16135643X-RAY DIFFRACTION99.9
2.34-2.490.18014520.15665652X-RAY DIFFRACTION99.98
2.49-2.680.17864620.16045651X-RAY DIFFRACTION99.97
2.68-2.950.18754610.16315696X-RAY DIFFRACTION99.98
2.95-3.370.16654550.14555656X-RAY DIFFRACTION99.95
3.37-4.250.13234580.12135685X-RAY DIFFRACTION99.79
4.25-42.090.13064700.12715756X-RAY DIFFRACTION99.41

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