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- PDB-6ibj: Copper binding protein from Laetisaria arvalis (LaX325) -

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Basic information

Entry
Database: PDB / ID: 6ibj
TitleCopper binding protein from Laetisaria arvalis (LaX325)
ComponentsAuxiliary activity CAZyme
KeywordsMETAL BINDING PROTEIN / Auxiliary activity CAZyme
Function / homologyCopper acquisition factor BIM1-like domain / Copper acquisition factor BIM1-like / Copper acquisition factor BIM1-like / side of membrane / extracellular region / plasma membrane / COPPER (II) ION / Lytic polysaccharide monooxygenase-like protein X325
Function and homology information
Biological speciesLaetisaria arvalis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFrandsen, K.E.H. / Tandrup, T. / Labourel, A. / Haon, M. / Berrin, J.-G. / Lo Leggio, L.
Funding support Denmark, France, 3items
OrganizationGrant numberCountry
Novo Nordisk FoundationNF17SA0027704 Denmark
The Carlsberg FoundationCF16-0673 & CF17-0533 Denmark
European Communitys Seventh Framework Programmegrant agreement 609398 France
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: A fungal family of lytic polysaccharide monooxygenase-like copper proteins.
Authors: Labourel, A. / Frandsen, K.E.H. / Zhang, F. / Brouilly, N. / Grisel, S. / Haon, M. / Ciano, L. / Ropartz, D. / Fanuel, M. / Martin, F. / Navarro, D. / Rosso, M.N. / Tandrup, T. / Bissaro, B. ...Authors: Labourel, A. / Frandsen, K.E.H. / Zhang, F. / Brouilly, N. / Grisel, S. / Haon, M. / Ciano, L. / Ropartz, D. / Fanuel, M. / Martin, F. / Navarro, D. / Rosso, M.N. / Tandrup, T. / Bissaro, B. / Johansen, K.S. / Zerva, A. / Walton, P.H. / Henrissat, B. / Leggio, L.L. / Berrin, J.G.
History
DepositionNov 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 4, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _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_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 24, 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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Auxiliary activity CAZyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6126
Polymers16,6641
Non-polymers9485
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint4 kcal/mol
Surface area7430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.920, 74.920, 64.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Auxiliary activity CAZyme


Mass: 16664.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Laetisaria arvalis (fungus) / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: A0A4P9I8G4*PLUS
#2: 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.: 4
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
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 mM L-Na-Glutamate, 20 mM DL-Alanine (racemic), 20 mM Glycine, 20 mM DL-Lysine HCl (racemic), 20 mM DL-Serine (racemic) 100 mM MES monohydrate pH 6.5 / 100 mM imidazole pH 6.5 20% (w/v) ...Details: 20 mM L-Na-Glutamate, 20 mM DL-Alanine (racemic), 20 mM Glycine, 20 mM DL-Lysine HCl (racemic), 20 mM DL-Serine (racemic) 100 mM MES monohydrate pH 6.5 / 100 mM imidazole pH 6.5 20% (w/v) PEG 500 MME and 10% (w/v) PEG 20.000.
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9799 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2018 / Details: Kirkpatrick-Baez (KB) mirror pair (VFM, HFM)
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 2.1→60 Å / Num. obs: 11173 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / CC1/2: 0.999 / Rrim(I) all: 0.087 / Net I/σ(I): 12.25
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 7.44 % / Mean I/σ(I) obs: 1.49 / Num. unique obs: 807 / CC1/2: 0.803 / Rrim(I) all: 0.1703 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IBI

6ibi


Resolution: 2.1→48.88 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.025 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.187 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25618 575 5.1 %RANDOM
Rwork0.19351 ---
obs0.19647 10600 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.919 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å2-0 Å2-0 Å2
2--2.2 Å2-0 Å2
3----4.39 Å2
Refinement stepCycle: 1 / Resolution: 2.1→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1125 0 57 55 1237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0141217
X-RAY DIFFRACTIONr_bond_other_d0.0010.018989
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.6251664
X-RAY DIFFRACTIONr_angle_other_deg0.8231.6172316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2325149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24724.19462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38715153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.578154
X-RAY DIFFRACTIONr_chiral_restr0.0540.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021404
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02242
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_it3.7695.577599
X-RAY DIFFRACTIONr_mcbond_other3.7675.568598
X-RAY DIFFRACTIONr_mcangle_it5.3048.348747
X-RAY DIFFRACTIONr_mcangle_other5.3028.358748
X-RAY DIFFRACTIONr_scbond_it4.6545.874618
X-RAY DIFFRACTIONr_scbond_other4.655.873619
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7148.696918
X-RAY DIFFRACTIONr_long_range_B_refined8.20166.0641262
X-RAY DIFFRACTIONr_long_range_B_other8.20365.971258
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 38 -
Rwork0.343 767 -
obs--99.51 %

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