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- PDB-6ydc: X-ray structure of LPMO -

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Basic information

Entry
Database: PDB / ID: 6ydc
TitleX-ray structure of LPMO
ComponentsLPMO lytic polysaccharide monooxygenase
KeywordsMETAL BINDING PROTEIN / Lytic Polysaccharide Monooxygenase / Complex / cellotetraose
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
beta-cellotetraose / beta-cellotriose / COPPER (II) ION / AA9 family lytic polysaccharide monooxygenase A
Similarity search - Component
Biological speciesCollariella virescens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTandrup, T. / Tryfona, T. / Frandsen, K.E.H. / Johansen, K.S. / Dupree, P. / Lo Leggio, L.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17SA0027704 Denmark
CitationJournal: Biochemistry / Year: 2020
Title: Oligosaccharide Binding and Thermostability of Two Related AA9 Lytic Polysaccharide Monooxygenases.
Authors: Tandrup, T. / Tryfona, T. / Frandsen, K.E.H. / Johansen, K.S. / Dupree, P. / Lo Leggio, L.
History
DepositionMar 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LPMO lytic polysaccharide monooxygenase
B: LPMO lytic polysaccharide monooxygenase
C: LPMO lytic polysaccharide monooxygenase
D: LPMO lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,64115
Polymers111,1654
Non-polymers2,47611
Water26,2301456
1
A: LPMO lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6174
Polymers27,7911
Non-polymers8263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LPMO lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6174
Polymers27,7911
Non-polymers8263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: LPMO lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4554
Polymers27,7911
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: LPMO lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9513
Polymers27,7911
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.790, 120.800, 136.360
Angle α, β, γ (deg.)90.000, 92.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
LPMO lytic polysaccharide monooxygenase


Mass: 27791.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Collariella virescens (fungus) / Gene: aa9 / Production host: Aspergillus oryzae (mold) / References: UniProt: A0A223GEC9

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Sugars , 2 types, 3 molecules

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


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 2
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
#3: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 1
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 , 3 types, 1464 molecules

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


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 1456 / 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: 2.95 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M NaCl, 0.1 M HEPES pH 6.5, 1.5 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.96 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 85419 / % possible obs: 98.4 % / Redundancy: 4.55 % / CC1/2: 0.989 / Net I/σ(I): 5.54
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.16 % / Mean I/σ(I) obs: 1.44 / Num. unique obs: 6184 / CC1/2: 0.544 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMACv5.8.0230refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ACH

5ach


Resolution: 2→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.26209 --
Rwork0.2146 --
obs0.21695 81172 98.39 %
Displacement parametersBiso max: 61.24 Å2 / Biso mean: 14.8197 Å2 / Biso min: 2.27 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6984 0 148 1457 8589

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