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- PDB-6ydf: X-ray structure of LPMO. -

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Basic information

Entry
Database: PDB / ID: 6ydf
TitleX-ray structure of LPMO.
ComponentsLPMO lytic polysaccharide monooxygenase
KeywordsMETAL BINDING PROTEIN / Lytic Polysaccharide Monooxygenase
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 speciesCollariella virescens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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 2.0Apr 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_ref_seq / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 2.1Mar 8, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 2.2Feb 7, 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: LPMO lytic polysaccharide monooxygenase
B: LPMO lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9987
Polymers55,5822
Non-polymers4155
Water4,306239
1
A: LPMO lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0474
Polymers27,7911
Non-polymers2563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 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)51.120, 39.390, 119.930
Angle α, β, γ (deg.)90.000, 93.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LPMO lytic polysaccharide monooxygenase


Mass: 27791.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Collariella virescens (fungus) / Gene: aa9 / Production host: Aspergillus oryzae (mold) / References: UniProt: A0A223GEC9
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / 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: 2.12→50 Å / Num. obs: 26050 / % possible obs: 94.5 % / Redundancy: 4.02 % / CC1/2: 0.995 / Net I/σ(I): 8.7
Reflection shellResolution: 2.12→2.18 Å / Num. unique obs: 1853 / CC1/2: 0.508

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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: 2.12→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.24944 --
Rwork0.19732 --
obs0.19979 24792 94.48 %
Displacement parametersBiso max: 92.8 Å2 / Biso mean: 17.3766 Å2 / Biso min: 8.13 Å2
Refinement stepCycle: LAST / Resolution: 2.12→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3492 0 17 241 3750

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