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- PDB-5ach: X-ray Structure of LPMO -

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Basic information

Entry
Database: PDB / ID: 5ach
TitleX-ray Structure of LPMO
ComponentsLYTIC POLYSACCHARIDE MONOOXYGENASE
KeywordsOXIDOREDUCTASE / 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
Coagulation Factor XIII; Chain A, domain 1 - #70 / Auxiliary Activity family 9 / : / Auxiliary Activity family 9 (formerly GH61) / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta
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: 1.28 Å
AuthorsFrandsen, K.E.H. / Poulsen, J.N. / Tovborg, M. / Johansen, K.S. / Lo Leggio, L.
CitationJournal: Nat. Chem. Biol. / Year: 2016
Title: The molecular basis of polysaccharide cleavage by lytic polysaccharide monooxygenases.
Authors: Frandsen, K.E. / Simmons, T.J. / Dupree, P. / Poulsen, J.C. / Hemsworth, G.R. / Ciano, L. / Johnston, E.M. / Tovborg, M. / Johansen, K.S. / von Freiesleben, P. / Marmuse, L. / Fort, S. / ...Authors: Frandsen, K.E. / Simmons, T.J. / Dupree, P. / Poulsen, J.C. / Hemsworth, G.R. / Ciano, L. / Johnston, E.M. / Tovborg, M. / Johansen, K.S. / von Freiesleben, P. / Marmuse, L. / Fort, S. / Cottaz, S. / Driguez, H. / Henrissat, B. / Lenfant, N. / Tuna, F. / Baldansuren, A. / Davies, G.J. / Lo Leggio, L. / Walton, P.H.
History
DepositionAug 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Jan 17, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: LYTIC POLYSACCHARIDE MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,08918
Polymers25,2731
Non-polymers81717
Water9,530529
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.700, 124.700, 124.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-2041-

HOH

21A-2076-

HOH

31A-2082-

HOH

41A-2083-

HOH

51A-2130-

HOH

61A-2229-

HOH

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Components

#1: Protein LYTIC POLYSACCHARIDE MONOOXYGENASE / LPMO


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*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#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: isolated from a genetically manipulated source
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.88 % / Description: NONE
Crystal growpH: 5.5
Details: 3.0M SODIUM CHLORIDE, 100MM CITRIC ACID PH3.5, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.28→41.57 Å / Num. obs: 85084 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9
Reflection shellResolution: 1.28→1.32 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.4 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EIR

4eir


Resolution: 1.28→41.57 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.335 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.14705 4228 5 %RANDOM
Rwork0.11751 ---
obs0.11903 80784 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.617 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.28→41.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 30 529 2347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192003
X-RAY DIFFRACTIONr_bond_other_d0.0010.021783
X-RAY DIFFRACTIONr_angle_refined_deg1.9711.9352786
X-RAY DIFFRACTIONr_angle_other_deg1.71634122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0085272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65825.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.18115265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.299157
X-RAY DIFFRACTIONr_chiral_restr0.1380.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212407
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02471
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7791.5131012
X-RAY DIFFRACTIONr_mcbond_other2.7781.5081011
X-RAY DIFFRACTIONr_mcangle_it3.1892.2831280
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4091.678991
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr6.133785
X-RAY DIFFRACTIONr_sphericity_free40.2975171
X-RAY DIFFRACTIONr_sphericity_bonded17.4254103
LS refinement shellResolution: 1.28→1.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 304 -
Rwork0.33 5861 -
obs--99.15 %

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