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- PDB-7ntl: AA9 lytic polysaccharide monooxygenase (LPMO) from Malbranchea ci... -

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Basic information

Entry
Database: PDB / ID: 7ntl
TitleAA9 lytic polysaccharide monooxygenase (LPMO) from Malbranchea cinnamomea
ComponentsLPMO9F
KeywordsMETAL BINDING PROTEIN / LPMO / monooxygenase
Function / homologyAuxiliary Activity family 9 / Auxiliary Activity family 9 (formerly GH61) / extracellular region / CITRIC ACID / COPPER (II) ION / LPMO9F
Function and homology information
Biological speciesMalbranchea cinnamomea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsMazurkewich, S. / Seveso, A. / Huttner, S. / Branden, G. / Larsbrink, L.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structure of a C1/C4-oxidizing AA9 lytic polysaccharide monooxygenase from the thermophilic fungus Malbranchea cinnamomea.
Authors: Mazurkewich, S. / Seveso, A. / Huttner, S. / Branden, G. / Larsbrink, J.
History
DepositionMar 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LPMO9F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4873
Polymers23,2311
Non-polymers2562
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-9 kcal/mol
Surface area9110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.956, 43.128, 52.341
Angle α, β, γ (deg.)90.000, 101.814, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein LPMO9F


Mass: 23231.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Asp10 cyclised to succinimde SNN / Source: (gene. exp.) Malbranchea cinnamomea (fungus) / Gene: lpmo9f / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168H / References: UniProt: A0A5J6BJN2
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.85 Å3/Da / Density % sol: 33.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 100 mM phosphate/citrate buffer at pH 4.2 with 100 mM NaCl and 23.5 % PEG 8000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.38→38.13 Å / Num. obs: 34403 / % possible obs: 92.26 % / Redundancy: 6.4 % / Biso Wilson estimate: 15.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06375 / Rrim(I) all: 0.06923 / Net I/σ(I): 13.69
Reflection shellResolution: 1.38→1.43 Å / Rmerge(I) obs: 0.8729 / Num. unique obs: 2911 / CC1/2: 0.715 / Rrim(I) all: 0.9922

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ha5

6ha5


Resolution: 1.38→38.13 Å / SU ML: 0.1285 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.16
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1928 1872 5.78 %
Rwork0.161 30512 -
obs0.1629 32384 92.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.83 Å2
Refinement stepCycle: LAST / Resolution: 1.38→38.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1633 0 14 243 1890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561744
X-RAY DIFFRACTIONf_angle_d0.90382408
X-RAY DIFFRACTIONf_chiral_restr0.0881248
X-RAY DIFFRACTIONf_plane_restr0.0067331
X-RAY DIFFRACTIONf_dihedral_angle_d9.1151951
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.420.3143960.30361607X-RAY DIFFRACTION63.59
1.42-1.460.26451220.26451951X-RAY DIFFRACTION76.83
1.46-1.510.23131320.22852187X-RAY DIFFRACTION86.47
1.51-1.560.27311380.20832283X-RAY DIFFRACTION91.05
1.56-1.620.22451430.19442375X-RAY DIFFRACTION93.54
1.62-1.70.22571510.17632397X-RAY DIFFRACTION94.48
1.7-1.790.19141510.16962441X-RAY DIFFRACTION96.68
1.79-1.90.1941510.16652482X-RAY DIFFRACTION98.21
1.9-2.040.18171530.16022524X-RAY DIFFRACTION98.86
2.04-2.250.1931580.15412540X-RAY DIFFRACTION99.63
2.25-2.580.18031570.16482542X-RAY DIFFRACTION99.85
2.58-3.250.18971580.16542571X-RAY DIFFRACTION99.93
3.25-38.130.17511620.12982612X-RAY DIFFRACTION99.86

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