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- PDB-7pz3: Structure of an LPMO at 5.37x10^3 Gy -

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Basic information

Entry
Database: PDB / ID: 7pz3
TitleStructure of an LPMO at 5.37x10^3 Gy
ComponentsGh61 isozyme a
KeywordsOXIDOREDUCTASE / Lytic polysaccharide monooxygenase / metalloenzyme / copper / Auxiliary activity
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / cellulase activity / cellulose catabolic process / extracellular region / metal ion binding
Similarity search - Function
Auxiliary Activity family 9 / : / Auxiliary Activity family 9 (formerly GH61)
Similarity search - Domain/homology
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: 1.9 Å
AuthorsTandrup, T. / Muderspach, S.J. / Ipsen, J.O. / Johansen, K.S. / Lo Leggio, L.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17SA0027704 Denmark
Danish Council for Independent Research8021-00273B Denmark
CitationJournal: Iucrj / Year: 2022
Title: Changes in active-site geometry on X-ray photoreduction of a lytic polysaccharide monooxygenase active-site copper and saccharide binding.
Authors: Tandrup, T. / Muderspach, S.J. / Banerjee, S. / Santoni, G. / Ipsen, J.O. / Hernandez-Rollan, C. / Norholm, M.H.H. / Johansen, K.S. / Meilleur, F. / Lo Leggio, L.
History
DepositionOct 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 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

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Assembly

Deposited unit
A: Gh61 isozyme a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0135
Polymers24,4181
Non-polymers5954
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.460, 87.400, 37.470
Angle α, β, γ (deg.)90.000, 104.900, 90.000
Int Tables number4
Space group name H-MP1211

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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 genetically manipulated source
Source: (gene. exp.) Thermoascus aurantiacus (fungus) / Production host: Aspergillus oryzae (mold) / References: UniProt: G3XAP7, cellulase
#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 , 4 types, 161 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
#3: Chemical ChemComp-AKR / ACRYLIC ACID


Mass: 72.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O2
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 44.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 mM MgCl2, 0.1 M HEPES pH 7.5, 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: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 16119 / % possible obs: 95.2 % / Redundancy: 1.99 % / CC1/2: 0.97 / Net I/σ(I): 3.08
Reflection shellResolution: 1.9→1.95 Å / Num. unique obs: 1194 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZUD

3zud


Resolution: 1.9→33.32 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 815 5.1 %RANDOM
Rwork0.2081 ---
obs0.2106 15301 95.22 %-
Solvent computationSolvent model: MASK
Displacement parametersBiso max: 59.08 Å2 / Biso mean: 20.367 Å2 / Biso min: 12.61 Å2
Refinement stepCycle: final / Resolution: 1.9→33.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 35 158 1913
Biso mean--35.89 23.56 -
Num. residues----227

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