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- PDB-7q1k: Crystal structure of the native AA9A LPMO from Thermoascus aurantiacus -

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Basic information

Entry
Database: PDB / ID: 7q1k
TitleCrystal structure of the native AA9A LPMO from Thermoascus aurantiacus
ComponentsGh61 isozyme a
KeywordsOXIDOREDUCTASE / LPMO / thermostability / copper-binding / monooxygenase / thermophilic fungus
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
COPPER (II) ION / AA9 family lytic polysaccharide monooxygenase A
Similarity search - Component
Biological speciesThermoascus aurantiacus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsYu, W. / Mohsin, I. / Li, D.C. / Papageorgiou, A.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31571949 China
CitationJournal: Catalysts / Year: 2022
Title: Purification and Structural Characterization of the Auxiliary Activity 9 Native Lytic Polysaccharide Monooxygenase from Thermoascus aurantiacus and Identification of Its C1- and C4-Oxidized Reaction Products
Authors: Yu, W. / Mohsin, I. / Papageorgiou, A.C. / Li, D.
History
DepositionOct 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gh61 isozyme a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1136
Polymers24,4181
Non-polymers6955
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-15 kcal/mol
Surface area9460 Å2
Unit cell
Length a, b, c (Å)37.690, 64.191, 88.533
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 / Sugars , 2 types, 2 molecules A

#1: Protein Gh61 isozyme a / TaAA9A / lytic polysaccharide monooxygenase


Mass: 24418.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermoascus aurantiacus (fungus) / References: UniProt: G3XAP7, cellulase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 311 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.19 Å3/Da / Density % sol: 43.91 % / Description: Thin needles grown as haystacks
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M HEPES-NaOH pH 7.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.36→44.36 Å / Num. obs: 43359 / % possible obs: 92.6 % / Redundancy: 12.9 % / Biso Wilson estimate: 13.75 Å2 / CC1/2: 0.998 / CC star: 1 / Rpim(I) all: 0.059 / Rrim(I) all: 0.218 / Net I/σ(I): 9.1
Reflection shellResolution: 1.36→1.41 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2631 / CC1/2: 0.25 / Rpim(I) all: 1.203 / Rrim(I) all: 2.9 / % possible all: 58.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
EDNAdata collection
Aimless0.5.27data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2yet

2yet


Resolution: 1.36→44.27 Å / SU ML: 0.1693 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.7883
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: ML with simulated annealing
RfactorNum. reflection% reflection
Rfree0.1852 2159 5 %
Rwork0.1505 41061 -
obs0.1523 43220 92.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.63 Å2
Refinement stepCycle: LAST / Resolution: 1.36→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 42 307 2070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00541861
X-RAY DIFFRACTIONf_angle_d0.86632570
X-RAY DIFFRACTIONf_chiral_restr0.084289
X-RAY DIFFRACTIONf_plane_restr0.0068338
X-RAY DIFFRACTIONf_dihedral_angle_d8.3467274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.390.4196740.36421344X-RAY DIFFRACTION46.04
1.39-1.430.35211330.28972555X-RAY DIFFRACTION87.53
1.43-1.470.2811430.2422717X-RAY DIFFRACTION93.71
1.47-1.510.25531470.212783X-RAY DIFFRACTION94.61
1.51-1.560.24171450.19212778X-RAY DIFFRACTION94.84
1.56-1.610.26141470.18292764X-RAY DIFFRACTION95.26
1.61-1.680.21251470.1662812X-RAY DIFFRACTION95.51
1.68-1.760.22821470.15182804X-RAY DIFFRACTION95.75
1.76-1.850.18321510.13472841X-RAY DIFFRACTION96.05
1.85-1.960.16671480.12722863X-RAY DIFFRACTION96.57
1.96-2.120.17121480.12752856X-RAY DIFFRACTION96.62
2.12-2.330.16271520.12572903X-RAY DIFFRACTION97.51
2.33-2.670.17531540.14152931X-RAY DIFFRACTION97.63
2.67-3.360.16851570.14052967X-RAY DIFFRACTION98.42
3.36-44.270.15441660.14123143X-RAY DIFFRACTION98.78

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