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- PDB-7pyi: Structure of LPMO in complex with cellotetraose at 6.65x10^6 Gy -

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Basic information

Entry
Database: PDB / ID: 7pyi
TitleStructure of LPMO in complex with cellotetraose at 6.65x10^6 Gy
ComponentsAuxiliary activity 9
KeywordsOXIDOREDUCTASE / lytic polysaccharide monooxygenase / metalloenzyme / AA9
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
beta-cellotetraose / COPPER (II) ION / AA9 family lytic polysaccharide monooxygenase A
Similarity search - Component
Biological speciesLentinus similis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 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)26,2605
Polymers25,2731
Non-polymers9874
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.010, 126.010, 126.010
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-464-

HOH

21A-465-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#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 , 3 types, 67 molecules

#3: 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.3 Å3/Da / Density % sol: 62.71 %
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: 2.05→89.1 Å / Num. obs: 21166 / % possible obs: 95.9 % / Redundancy: 3.29 % / CC1/2: 0.99 / Net I/σ(I): 15.87
Reflection shellResolution: 2.05→2.1 Å / Num. unique obs: 1596 / CC1/2: 0.48

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ACH

5ach


Resolution: 2.05→89.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1102 5.2 %RANDOM
Rwork0.218 ---
obs0.2204 20133 96.19 %-
Solvent computationSolvent model: MASK
Displacement parametersBiso max: 165.51 Å2 / Biso mean: 53.726 Å2 / Biso min: 28.38 Å2
Refinement stepCycle: final / Resolution: 2.05→89.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 61 68 1917
Biso mean--65.5 54.25 -
Num. residues----235
LS refinement shellResolution: 2.05→2.103 Å
RfactorNum. reflection% reflection
Rfree0.357 --
Rwork0.349 --
obs-1475 97.18 %

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