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- PDB-8b4g: Structure of a fungal LPMO bound to ligands -

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Basic information

Entry
Database: PDB / ID: 8b4g
TitleStructure of a fungal LPMO bound to ligands
ComponentsGh61 isozyme a
KeywordsOXIDOREDUCTASE / Monooxygenase / dihydroxyacetone / Lytic Polysaccharide Monooxygenase / Thermoascus aurantiacus
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / cellulase activity / cellulose catabolic process / monooxygenase activity / extracellular region / metal ion binding
Similarity search - Function
Auxiliary Activity family 9 / : / Auxiliary Activity family 9 (formerly GH61)
Similarity search - Domain/homology
Dihydroxyacetone / ACRYLIC ACID / COPPER (II) ION / AA9 family lytic polysaccharide monooxygenase A
Similarity search - Component
Biological speciesThermoascus aurantiacus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.496 Å
AuthorsBanerjee, S. / Huang, Z. / Brander, S. / Johansen, K.S. / Lo Leggio, L.
Funding support Denmark, Sweden, 3items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
Danish Council for Independent Research Denmark
Swedish Research Council Sweden
CitationJournal: To Be Published
Title: Structure of a fungal LPMO bound to ligands
Authors: Banerjee, S. / Huang, Z. / Brander, S. / Johansen, K.S. / Lo Leggio, L.
History
DepositionSep 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Gh61 isozyme a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0088
Polymers24,4181
Non-polymers5907
Water4,954275
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-20 kcal/mol
Surface area9930 Å2
Unit cell
Length a, b, c (Å)34.402, 87.312, 37.482
Angle α, β, γ (deg.)90.000, 104.812, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Gh61 isozyme a


Mass: 24418.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoascus aurantiacus (fungus) / Production host: Aspergillus oryzae (mold) / References: UniProt: G3XAP7, cellulase

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Sugars , 2 types, 2 molecules

#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
#5: Sugar ChemComp-2HA / Dihydroxyacetone


Type: saccharide / Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 280 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-AKR / ACRYLIC ACID


Mass: 72.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 20m M MgCl2 and 22 %(w/v) polyacrylic acid 5100 sodium salt

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jun 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.496→87.31 Å / Num. obs: 34235 / % possible obs: 99.3 % / Redundancy: 6.6 % / CC1/2: 0.996 / Net I/σ(I): 7.9
Reflection shellResolution: 1.5→1.52 Å / Num. unique obs: 1426 / CC1/2: 0.509

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZUD

3zud


Resolution: 1.496→43.656 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.168 / WRfactor Rwork: 0.138 / SU B: 1.575 / SU ML: 0.055 / Average fsc free: 0.9201 / Average fsc work: 0.927 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.071
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1809 1711 5.002 %
Rwork0.1486 32495 -
all0.15 --
obs-34206 99.211 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.843 Å2
Baniso -1Baniso -2Baniso -3
1--0.706 Å2-0 Å20.398 Å2
2--0.004 Å20 Å2
3---0.432 Å2
Refinement stepCycle: LAST / Resolution: 1.496→43.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1724 0 33 277 2034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131947
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171665
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.6562707
X-RAY DIFFRACTIONr_angle_other_deg1.4381.5733921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4165263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37424.94489
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.743102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84315262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.768153
X-RAY DIFFRACTIONr_chiral_restr0.0850.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022281
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02368
X-RAY DIFFRACTIONr_nbd_refined0.2270.2330
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21532
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2889
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2759
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2166
X-RAY DIFFRACTIONr_metal_ion_refined0.0630.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1190.215
X-RAY DIFFRACTIONr_nbd_other0.1950.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.230
X-RAY DIFFRACTIONr_mcbond_it1.2461.406979
X-RAY DIFFRACTIONr_mcbond_other1.21.392973
X-RAY DIFFRACTIONr_mcangle_it1.8542.0991234
X-RAY DIFFRACTIONr_mcangle_other1.8382.0951232
X-RAY DIFFRACTIONr_scbond_it2.091.579968
X-RAY DIFFRACTIONr_scbond_other2.0891.579968
X-RAY DIFFRACTIONr_scangle_it3.1032.3011462
X-RAY DIFFRACTIONr_scangle_other3.1022.3021463
X-RAY DIFFRACTIONr_lrange_it4.8718.0752119
X-RAY DIFFRACTIONr_lrange_other4.86918.072120
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.496-1.5350.281130.27521620.27525230.7820.77290.17040.271
1.535-1.5770.2841260.25923730.2625010.8220.82999.920.25
1.577-1.6230.2691200.23222900.23324100.8440.8711000.22
1.623-1.6720.2041140.21121940.21123080.8980.91000.198
1.672-1.7270.211210.221650.20122860.9220.9151000.184
1.727-1.7880.2041010.17920890.1821900.9270.931000.16
1.788-1.8550.2491040.17120060.17521110.9070.9399.95260.154
1.855-1.9310.1921040.15419270.15620320.9450.95699.95080.136
1.931-2.0160.157980.14618660.14619650.9640.96699.94910.132
2.016-2.1150.149930.13817810.13918740.970.9711000.126
2.115-2.2290.164910.13116770.13217680.9660.9741000.119
2.229-2.3630.173850.12415990.12616840.960.9741000.114
2.363-2.5260.19790.12815060.13115850.9520.971000.119
2.526-2.7280.188720.1314140.13214860.9580.9711000.121
2.728-2.9870.143670.12112800.12213470.9750.9791000.118
2.987-3.3380.155640.13211780.13312420.9710.9761000.13
3.338-3.850.177570.11710410.1210980.9710.9791000.121
3.85-4.7060.146460.1088760.119230.9760.98499.89170.117
4.706-6.6170.142360.1396820.1397180.9830.9831000.148
6.617-43.6560.176200.1813890.1814170.9720.96498.08150.2

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