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- PDB-7pz0: Structure of LPMO (expressed in E.coli) with cellotriose at 9.81x... -

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Basic information

Entry
Database: PDB / ID: 7pz0
TitleStructure of LPMO (expressed in E.coli) with cellotriose at 9.81x10^6 Gy
ComponentsAuxiliary activity 9
KeywordsOXIDOREDUCTASE / lytic polysaccharide monooxygenase / metalloenzyme / copper / auxiliary activity
Function / homology
Function and homology information


cellulose binding / cellulase / 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
beta-cellotriose / ACETATE ION / COPPER (II) ION / AA9 family lytic polysaccharide monooxygenase A
Similarity search - Component
Biological speciesPanus similis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 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: Auxiliary activity 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7159
Polymers25,2601
Non-polymers1,4558
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-39 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.900, 48.900, 108.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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Protein / Sugars , 2 types, 3 molecules A

#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.) Panus similis (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S2GKZ1
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 283 molecules

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


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
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 silicon:paraffin 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: 1.0332 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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 142855 / % possible obs: 90.6 % / Redundancy: 1.61 % / CC1/2: 0.99 / Net I/σ(I): 19.53
Reflection shellResolution: 1.2→1.23 Å / Num. unique obs: 10325 / CC1/2: 0.98

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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: 1.2→44.65 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.98 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1475 3930 5 %RANDOM
Rwork0.1339 ---
obs0.1347 74682 98.81 %-
Solvent computationSolvent model: MASK
Displacement parametersBiso max: 66.25 Å2 / Biso mean: 13.556 Å2 / Biso min: 7.48 Å2
Refinement stepCycle: final / Resolution: 1.2→44.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 89 278 2154
Biso mean--31.59 25.82 -
Num. residues----235

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