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

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Basic information

Entry
Database: PDB / ID: 6ibi
TitleCopper binding protein from Laetisaria arvalis (LaX325)
ComponentsAuxiliary activity CAZyme
KeywordsMETAL BINDING PROTEIN / Auxiliary activity CAZyme
Function / homology
Function and homology information


side of membrane / extracellular region / plasma membrane
Similarity search - Function
Copper acquisition factor BIM1-like domain / Copper acquisition factor BIM1-like / Copper acquisition factor BIM1-like
Similarity search - Domain/homology
COPPER (II) ION / IMIDAZOLE / TRIETHYLENE GLYCOL / Lytic polysaccharide monooxygenase-like protein X325
Similarity search - Component
Biological speciesLaetisaria arvalis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 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 Carslberg 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 1.1Nov 27, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Jan 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 1.3Mar 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 1.4Jul 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_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Auxiliary activity CAZyme
B: Auxiliary activity CAZyme
C: Auxiliary activity CAZyme
D: Auxiliary activity CAZyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,47839
Polymers66,6564
Non-polymers6,82235
Water9,890549
1
A: Auxiliary activity CAZyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,68211
Polymers16,6641
Non-polymers2,01810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Auxiliary activity CAZyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,36210
Polymers16,6641
Non-polymers1,6989
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Auxiliary activity CAZyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,36210
Polymers16,6641
Non-polymers1,6989
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Auxiliary activity CAZyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0728
Polymers16,6641
Non-polymers1,4087
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.599, 84.635, 127.319
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 149
2010B1 - 149
1020A1 - 152
2020C1 - 152
1030A1 - 148
2030D1 - 148
1040B1 - 149
2040C1 - 149
1050B1 - 148
2050D1 - 148
1060C1 - 148
2060D1 - 148

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein / Sugars , 2 types, 27 molecules ABCD

#1: Protein
Auxiliary activity CAZyme


Mass: 16664.023 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Laetisaria arvalis (fungus) / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: A0A4P9I8G4*PLUS
#3: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 23
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

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Non-polymers , 5 types, 561 molecules

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


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O

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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: 3.42 Å3/Da / Density % sol: 64.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MRC plates with 1:1 ratio drops (enzyme:reservoir solution) and 100 ul reservoir using an Oryx-8 robot. Protein: 13.3 mg/ml in 20 mM MES pH 6.0. Reservoir: 20 mM L-Na-Glutamate, 20 mM DL- ...Details: MRC plates with 1:1 ratio drops (enzyme:reservoir solution) and 100 ul reservoir using an Oryx-8 robot. Protein: 13.3 mg/ml in 20 mM MES pH 6.0. Reservoir: 20 mM L-Na-Glutamate, 20 mM DL-Alanine (racemic), 20 mM Glycine, 20 mM DL-Lysine HCl (racemic), 20 mM DL-Serine (racemic), 50 mM MES monohydrate pH 6.5, 50 mM imidazole pH 6.5. 20% (w/v) PEG 500 MME and 10% (w/v) PEG 20000.
PH range: 6.0-6.5 / Temp details: room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.299 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 6, 2018
RadiationMonochromator: Si[111] monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.299 Å / Relative weight: 1
ReflectionResolution: 2.08→100 Å / Num. obs: 57268 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 14 % / CC1/2: 0.998 / Rrim(I) all: 0.152 / Net I/σ(I): 12.93
Reflection shellResolution: 2.08→2.13 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 1.07 / Num. unique obs: 4005 / CC1/2: 0.744 / Rrim(I) all: 1.398 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
AutoSolphasing
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.08→42.35 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.927 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.186 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27087 2641 4.8 %RANDOM
Rwork0.24417 ---
obs0.2454 52714 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.444 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20 Å2
2--1.78 Å2-0 Å2
3----2.82 Å2
Refinement stepCycle: 1 / Resolution: 2.08→42.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4569 0 386 549 5504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0155146
X-RAY DIFFRACTIONr_bond_other_d0.0020.0184172
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.6277030
X-RAY DIFFRACTIONr_angle_other_deg2.4121.639792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6985617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88424.17259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25415627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4471516
X-RAY DIFFRACTIONr_chiral_restr0.0630.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025877
X-RAY DIFFRACTIONr_gen_planes_other0.0470.021021
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_it3.4484.2382441
X-RAY DIFFRACTIONr_mcbond_other3.4464.2362440
X-RAY DIFFRACTIONr_mcangle_it4.8336.3453049
X-RAY DIFFRACTIONr_mcangle_other4.8326.3483050
X-RAY DIFFRACTIONr_scbond_it4.2374.7962705
X-RAY DIFFRACTIONr_scbond_other4.2374.7962705
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2267.0693976
X-RAY DIFFRACTIONr_long_range_B_refined8.35253.1935644
X-RAY DIFFRACTIONr_long_range_B_other8.35353.2025645
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A45400.09
12B45400.09
21A44960.12
22C44960.12
31A44900.1
32D44900.1
41B44210.1
42C44210.1
51B44220.1
52D44220.1
61C44280.09
62D44280.09
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.484 213 -
Rwork0.448 3752 -
obs--97.78 %

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