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

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Basic information

Entry
Database: PDB / ID: 9fnh
TitleThe glycoside hydrolase family 71 (GH71) member AnGH71C from Aspergillus nidulans in complex with nigerotetraose.
ComponentsGlycoside hydrolase family 71
KeywordsCARBOHYDRATE / alpha-glucan / hydrolase / mutan / nigeran
Function / homologyglucan endo-1,3-alpha-glucosidase / glucan endo-1,3-alpha-glucosidase activity / Glycoside hydrolase family 71 / Glycosyl hydrolase family 71 / carbohydrate catabolic process / extracellular region / CITRIC ACID / TRIETHYLENE GLYCOL / glucan endo-1,3-alpha-glucosidase
Function and homology information
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsMazurkewich, S. / Widen, T. / Branden, G. / Larsbrink, J.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2020-03618 Sweden
CitationJournal: To Be Published
Title: The glycoside hydrolase family 71 (GH71) member AnGH71C from Aspergillus nidulans in complex with nigerotetraose.
Authors: Mazurkewich, S. / Widen, T. / Branden, G. / Larsbrink, J.
History
DepositionJun 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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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
C: Glycoside hydrolase family 71
D: Glycoside hydrolase family 71
X: Glycoside hydrolase family 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,86518
Polymers241,0555
Non-polymers4,81013
Water12,394688
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15860 Å2
ΔGint63 kcal/mol
Surface area56100 Å2
Unit cell
Length a, b, c (Å)80.273, 82.242, 87.069
Angle α, β, γ (deg.)103.520, 105.635, 117.592
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 5 molecules ABCDX

#1: Protein
Glycoside hydrolase family 71


Mass: 48211.035 Da / Num. of mol.: 5
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

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Sugars , 4 types, 8 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-3DGlcpa1-3DGlcpa1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a3-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][a-D-Glcp]{[(3+1)][a-D-Glcp]{[(3+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide
alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-3DGlcpa1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][a-D-Glcp]{[(3+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-3DGlcpa1-3DGlcpa1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2-2/a3-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][a-D-Glcp]{[(3+1)][a-D-Glcp]{[(3+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 693 molecules

#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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

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: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.916→41.7 Å / Num. obs: 82756 / % possible obs: 92.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 24.75 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.136 / Net I/σ(I): 6.4
Reflection shellResolution: 1.916→2.116 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4138 / CC1/2: 0.524 / % possible all: 65.5

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→41.7 Å / SU ML: 0.2315 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.1358
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2202 6245 7.55 %
Rwork0.1652 76487 -
obs0.1693 82732 62.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.95 Å2
Refinement stepCycle: LAST / Resolution: 1.92→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12697 0 323 688 13708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008913469
X-RAY DIFFRACTIONf_angle_d1.137118417
X-RAY DIFFRACTIONf_chiral_restr0.27672005
X-RAY DIFFRACTIONf_plane_restr0.00752357
X-RAY DIFFRACTIONf_dihedral_angle_d16.23034760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.940.273730.264537X-RAY DIFFRACTION0.91
1.94-1.960.2905190.2288107X-RAY DIFFRACTION2.89
1.96-1.980.267260.2379276X-RAY DIFFRACTION6.9
1.98-2.010.25400.2531412X-RAY DIFFRACTION10.31
2.01-2.040.2745510.2488583X-RAY DIFFRACTION14.55
2.04-2.060.2803720.2446727X-RAY DIFFRACTION17.95
2.06-2.090.3284690.2422903X-RAY DIFFRACTION22.34
2.09-2.120.3011720.22921081X-RAY DIFFRACTION26.07
2.13-2.160.32221020.22681324X-RAY DIFFRACTION32.12
2.16-2.190.25941200.22391705X-RAY DIFFRACTION41.59
2.19-2.230.27852080.23042041X-RAY DIFFRACTION49.97
2.23-2.270.30881910.23012220X-RAY DIFFRACTION55.25
2.27-2.320.25932270.22532371X-RAY DIFFRACTION59.63
2.32-2.360.29542220.22832644X-RAY DIFFRACTION63.96
2.36-2.410.28412400.21612739X-RAY DIFFRACTION66.97
2.41-2.470.24772300.21322948X-RAY DIFFRACTION72.36
2.47-2.530.23542440.20873156X-RAY DIFFRACTION77.95
2.53-2.60.27072580.20493418X-RAY DIFFRACTION83.05
2.6-2.680.26173010.20813704X-RAY DIFFRACTION90.55
2.68-2.760.25853260.20563919X-RAY DIFFRACTION95.87
2.76-2.860.26083260.19653998X-RAY DIFFRACTION98.38
2.86-2.980.25483110.18424052X-RAY DIFFRACTION98.18
2.98-3.110.24073280.18064026X-RAY DIFFRACTION98.35
3.11-3.280.22823230.1554008X-RAY DIFFRACTION98.34
3.28-3.480.22653110.1464047X-RAY DIFFRACTION98.22
3.48-3.750.20013330.13053993X-RAY DIFFRACTION98.25
3.75-4.130.16053250.12273998X-RAY DIFFRACTION98.09
4.13-4.720.1733130.11434035X-RAY DIFFRACTION98.42
4.72-5.950.17263250.1324017X-RAY DIFFRACTION98.46
5.95-41.70.18333290.15873998X-RAY DIFFRACTION97.94

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