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- PDB-9exj: Crystal structure of Aspergillus fumigatus AA11 Lytic Polysacchar... -

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Basic information

Entry
Database: PDB / ID: 9exj
TitleCrystal structure of Aspergillus fumigatus AA11 Lytic Polysaccharide Monooxygenase (AfAA11B) in complex with Cu(II)
ComponentsEndoglucanase
KeywordsMETAL BINDING PROTEIN / Lytic polysaccharide monooxygenase / copper-binding protein
Function / homologyOxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous / cellulose catabolic process / monooxygenase activity / extracellular region / metal ion binding / COPPER (II) ION / AA11 family lytic polysaccharide monooxygenase B
Function and homology information
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHall, K.R. / Ronnekleiv, S.E. / Skaali, R. / Rieder, L. / Englund, A.N.B. / Dalleywater, E.L. / Ayuso-Fernandez, I. / Golten, O. / Rohr, A.K. / Sorlie, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)856446European Union
CitationJournal: To Be Published
Title: Surface topology prevents efficient chitin degradation for a clade of LPMOs
Authors: Hall, K.R. / Ronnekleiv, S.E. / Skaali, R. / Rieder, L. / Englund, A.N.B. / Dalleywater, E.L. / Ayuso-Fernandez, I. / Golten, O. / Rohr, A.K. / Sorlie, M.
History
DepositionApr 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 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: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7884
Polymers23,4071
Non-polymers3813
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-16 kcal/mol
Surface area8920 Å2
Unit cell
Length a, b, c (Å)46.414, 53.777, 71.834
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Endoglucanase


Mass: 23407.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: AFUA_5G03010 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q4WEH3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 8.5, 2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.4→43.05 Å / Num. obs: 36084 / % possible obs: 99.9 % / Redundancy: 1.9 % / Biso Wilson estimate: 10.48 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.1
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1748 / CC1/2: 0.631

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Processing

Software
NameVersionClassification
REFMAC1.19_4092refinement
autoPROC1.19_4092data reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→43.05 Å / SU ML: 0.1444 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 18.0692
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1907 1767 4.9 %
Rwork0.1512 34313 -
obs0.1531 36080 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.21 Å2
Refinement stepCycle: LAST / Resolution: 1.4→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 20 223 1691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651549
X-RAY DIFFRACTIONf_angle_d1.04272116
X-RAY DIFFRACTIONf_chiral_restr0.095227
X-RAY DIFFRACTIONf_plane_restr0.0089286
X-RAY DIFFRACTIONf_dihedral_angle_d6.7142216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.32941310.27422561X-RAY DIFFRACTION99.01
1.44-1.480.26071440.22762585X-RAY DIFFRACTION99.71
1.48-1.530.24281540.18112594X-RAY DIFFRACTION100
1.53-1.580.22191410.16652610X-RAY DIFFRACTION99.96
1.58-1.650.22121310.14792590X-RAY DIFFRACTION99.96
1.65-1.720.18491330.13212631X-RAY DIFFRACTION100
1.72-1.810.19361420.11912603X-RAY DIFFRACTION99.89
1.81-1.930.20951270.12752651X-RAY DIFFRACTION100
1.93-2.070.18281260.12012633X-RAY DIFFRACTION100
2.07-2.280.13961160.12092650X-RAY DIFFRACTION100
2.28-2.610.17941450.14342682X-RAY DIFFRACTION100
2.61-3.290.17951160.15242707X-RAY DIFFRACTION99.86
3.29-43.050.17191610.16272816X-RAY DIFFRACTION100

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