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- PDB-7pxk: X-ray structure of LPMO at 1.39x10^5 Gy -

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Basic information

Entry
Database: PDB / ID: 7pxk
TitleX-ray structure of LPMO at 1.39x10^5 Gy
ComponentsAuxiliary activity 9
KeywordsOXIDOREDUCTASE / lytic polysaccharide monooxygenase / metalloenzyme / AA9
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / 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 speciesLentinus similis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTandrup, T. / 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 8, 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: Auxiliary activity 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5583
Polymers25,2731
Non-polymers2852
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-9 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.990, 124.990, 124.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-693-

HOH

21A-696-

HOH

31A-698-

HOH

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Components

#1: Protein Auxiliary activity 9 / LsAA9A / lytic polysaccharide monooxygenase


Mass: 25272.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lentinus similis (fungus) / Production host: Aspergillus oryzae (mold)
References: UniProt: A0A0S2GKZ1, lytic cellulose monooxygenase (C4-dehydrogenating)
#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: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
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: 3.22 Å3/Da / Density % sol: 61.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 3.3 M NaCl, 0.1 M Citric acid pH 3.5

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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 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 124225 / % possible obs: 100 % / Redundancy: 5.07 % / CC1/2: 0.99 / Net I/σ(I): 17.33
Reflection shellResolution: 1.4→1.44 Å / Mean I/σ(I) obs: 1.23 / Num. unique obs: 9227 / CC1/2: 0.48

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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: 5ACH

5ach


Resolution: 1.4→44.23 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 3284 5 %RANDOM
Rwork0.1868 ---
obs0.1878 62586 99.93 %-
Solvent computationSolvent model: MASK
Displacement parametersBiso max: 289.74 Å2 / Biso mean: 16.642 Å2 / Biso min: 8.76 Å2
Refinement stepCycle: final / Resolution: 1.4→44.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 15 311 2114
Biso mean--22.71 27.73 -
Num. residues----235
LS refinement shellResolution: 1.4→1.436 Å

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