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- PDB-9hdg: The structure of the catalytic domain of AfAA11B from the filamen... -

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Basic information

Entry
Database: PDB / ID: 9hdg
TitleThe structure of the catalytic domain of AfAA11B from the filamentous fungus Aspergillus fumigatus
ComponentsAA11 family lytic polysaccharide monooxygenase B
KeywordsOXIDOREDUCTASE / Lytic Polysaccharide Monooxygenase / Chitin / Tetraacetyl-Chitotetraose / Auxillary Activity family / AA11 / Aspergillus Fumigatus / LPMO
Function / homologyOxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous / cellulose catabolic process / monooxygenase activity / extracellular region / metal ion binding / ASCORBIC ACID / COPPER (II) ION / AA11 family lytic polysaccharide monooxygenase B
Function and homology information
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsHall, K. / Roennekleiv, S.E. / Gautieri, A. / Skaali, R. / Rieder, L. / Englund, A.N. / Landsem, E. / Emrich-Mills, T. / Ayuso-Fernandez, I. / Golten, O. ...Hall, K. / Roennekleiv, S.E. / Gautieri, A. / Skaali, R. / Rieder, L. / Englund, A.N. / Landsem, E. / Emrich-Mills, T. / Ayuso-Fernandez, I. / Golten, O. / Kjendseth, A.R. / Soerlie, M. / Eijsink, V.G.H.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)856446European Union
Citation
Journal: Acs Catalysis / Year: 2025
Title: Structure-Function Analysis of an Understudied Type of LPMO with Unique Redox Properties and Substrate Specificity.
Authors: Hall, K.R. / Elisa Ronnekleiv, S. / Gautieri, A. / Lilleas, H. / Skaali, R. / Rieder, L. / Nikoline Englund, A. / Landsem, E. / Emrich-Mills, T.Z. / Ayuso-Fernandez, I. / Kjendseth Rohr, A. ...Authors: Hall, K.R. / Elisa Ronnekleiv, S. / Gautieri, A. / Lilleas, H. / Skaali, R. / Rieder, L. / Nikoline Englund, A. / Landsem, E. / Emrich-Mills, T.Z. / Ayuso-Fernandez, I. / Kjendseth Rohr, A. / Sorlie, M. / Eijsink, V.G.H.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionNov 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 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: AA11 family lytic polysaccharide monooxygenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,44410
Polymers23,4071
Non-polymers1,0379
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-57 kcal/mol
Surface area9240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.332, 53.655, 70.929
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

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Protein , 1 types, 1 molecules A

#1: Protein AA11 family lytic polysaccharide monooxygenase B / LPMO11B


Mass: 23407.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: AA11B, AFUA_5G03010 / Production host: Komagataella pastoris (fungus)
References: UniProt: Q4WEH3, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous

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Sugars , 2 types, 2 molecules

#3: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Comment: medication*YM
#4: 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

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Non-polymers , 3 types, 221 molecules

#2: 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.69 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Tris, Ammonium sulphate / Temp details: Grown at room temerature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.873 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 4, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.26→35.46 Å / Num. obs: 47610 / % possible obs: 98.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 15.98 Å2 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.038 / Rrim(I) all: 0.065 / Χ2: 0.96 / Net I/σ(I): 10.5
Reflection shellResolution: 1.26→1.3 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.405 / Num. unique obs: 4611 / CC1/2: 0.331 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
Aimless0.7.15data scaling
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→35.46 Å / SU ML: 0.1683 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8306
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1959 2000 4.23 %
Rwork0.1645 45227 -
obs0.1659 47227 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.36 Å2
Refinement stepCycle: LAST / Resolution: 1.26→35.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1483 0 57 214 1754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591655
X-RAY DIFFRACTIONf_angle_d0.91482275
X-RAY DIFFRACTIONf_chiral_restr0.0908239
X-RAY DIFFRACTIONf_plane_restr0.0066311
X-RAY DIFFRACTIONf_dihedral_angle_d8.0431238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.290.36471330.34023008X-RAY DIFFRACTION92.27
1.29-1.330.29471420.30763191X-RAY DIFFRACTION97.37
1.33-1.370.33031430.2913239X-RAY DIFFRACTION98.69
1.37-1.410.31021420.25173241X-RAY DIFFRACTION98.66
1.41-1.460.23591440.20883234X-RAY DIFFRACTION99.21
1.46-1.520.23631440.18133254X-RAY DIFFRACTION99.33
1.52-1.590.2131440.1633264X-RAY DIFFRACTION98.98
1.59-1.670.20321450.1593269X-RAY DIFFRACTION99.16
1.67-1.780.18791370.14873113X-RAY DIFFRACTION94.34
1.78-1.910.20441420.14623199X-RAY DIFFRACTION96.42
1.91-2.110.18691450.14153286X-RAY DIFFRACTION99.13
2.11-2.410.18651460.14633296X-RAY DIFFRACTION98.71
2.41-3.040.19911460.16973302X-RAY DIFFRACTION97.62
3.04-35.460.16141470.14883331X-RAY DIFFRACTION94.08

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