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- PDB-7pym: Structure of an LPMO (expressed in E.coli) at 5.61x10^4 Gy -

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Basic information

Entry
Database: PDB / ID: 7pym
TitleStructure of an LPMO (expressed in E.coli) at 5.61x10^4 Gy
ComponentsAuxiliary activity 9
KeywordsOXIDOREDUCTASE / Lytic polysaccharide monooxygenase / metalloenzyme / copper / Auxiliary activity
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / hydrolase activity, acting on glycosyl bonds / 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
COPPER (II) ION / AA9 family lytic polysaccharide monooxygenase A
Similarity search - Component
Biological speciesLentinus similis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsTandrup, T. / Muderspach, S.J. / Banerjee, S. / Ipsen, J.O. / Rollan, C.H. / Norholm, M.H.H. / 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 10, 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)25,7086
Polymers25,2601
Non-polymers4485
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-55 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.860, 48.860, 108.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 25259.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lentinus similis (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S2GKZ1
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 278 K / Method: batch mode / pH: 4.5
Details: 2.3 M ammonium sulfate, 0.1 M sodium acetate pH 4.5 Under a layer of Paraffin:Silicon oil in a 3:2 ratio

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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: 1.75→50 Å / Num. obs: 47775 / % possible obs: 94 % / Redundancy: 1.62 % / CC1/2: 0.99 / Net I/σ(I): 4.66
Reflection shellResolution: 1.75→1.8 Å / Num. unique obs: 3449 / CC1/2: 0.64

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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: 7PQR

7pqr


Resolution: 1.75→44.62 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 1284 5 %RANDOM
Rwork0.1653 ---
obs0.1668 24341 99.62 %-
Solvent computationSolvent model: MASK
Displacement parametersBiso max: 70.19 Å2 / Biso mean: 17.461 Å2 / Biso min: 11.6 Å2
Refinement stepCycle: final / Resolution: 1.75→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 21 260 2068
Biso mean--51.65 26.75 -
Num. residues----235

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