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

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Basic information

Entry
Database: PDB / ID: 6ibh
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 / COPPER (II) ION / IMIDAZOLE / Lytic polysaccharide monooxygenase-like protein X325
Function and homology information
Biological speciesLaetisaria arvalis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 1.1Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,95816
Polymers33,3282
Non-polymers2,62914
Water3,369187
1
A: Auxiliary activity CAZyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9038
Polymers16,6641
Non-polymers1,2397
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Auxiliary activity CAZyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0558
Polymers16,6641
Non-polymers1,3917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.940, 67.590, 68.900
Angle α, β, γ (deg.)90.00, 97.94, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 148
2010B1 - 148

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Components

#1: Protein Auxiliary activity CAZyme


Mass: 16664.023 Da / Num. of mol.: 2
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
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
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 / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1:1 ratio of protein:reservoir solution in MRC plates using an Oryx-8 robot. Protein concentration: 13.3 mg/ml Reservoir solution (Morpheus screen #40): 12.5 (w/v)MPD, 12.5 (w/v)PEG1000, 12. ...Details: 1:1 ratio of protein:reservoir solution in MRC plates using an Oryx-8 robot. Protein concentration: 13.3 mg/ml Reservoir solution (Morpheus screen #40): 12.5 (w/v)MPD, 12.5 (w/v)PEG1000, 12.5 (w/v)PEG3350. 20mM 1,6-hexanediol, 20mM 1-butanol, 20mM (RS)1,2-propandiol, 20mM 2-propanol, 20mM 1,4-butandiol, 20mM 1,3-propandiol. 50 mM MES monohydrate pH 6.5, 50 mM imidazole pH 6.5.
PH range: 6.5 / Temp details: room

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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
RadiationMonochromator: Si (111), double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 1.82→68.25 Å / Num. obs: 25629 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / CC1/2: 0.997 / Rrim(I) all: 0.097 / Net I/σ(I): 11.79
Reflection shellResolution: 1.82→1.87 Å / Redundancy: 6.3 % / Num. unique obs: 1351 / CC1/2: 0.816 / Rrim(I) all: 0.911 / % possible all: 68.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0230refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→68.24 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.325 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20753 1287 5 %RANDOM
Rwork0.16711 ---
obs0.1691 24384 94.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.953 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å2-2.69 Å2
2--2.11 Å2-0 Å2
3----1.05 Å2
Refinement stepCycle: 1 / Resolution: 1.82→68.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 161 187 2588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0142533
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182045
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.6233472
X-RAY DIFFRACTIONr_angle_other_deg0.9391.614803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.8445.19316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80824.524126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97715310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.939158
X-RAY DIFFRACTIONr_chiral_restr0.0660.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023151
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02504
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_it2.933.6741222
X-RAY DIFFRACTIONr_mcbond_other2.9283.6711221
X-RAY DIFFRACTIONr_mcangle_it3.9115.5051529
X-RAY DIFFRACTIONr_mcangle_other3.915.5081530
X-RAY DIFFRACTIONr_scbond_it3.7984.1291311
X-RAY DIFFRACTIONr_scbond_other3.7974.1311312
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5556.0871941
X-RAY DIFFRACTIONr_long_range_B_refined6.5745.572678
X-RAY DIFFRACTIONr_long_range_B_other6.56945.5722679
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4602 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.817→1.864 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 72 -
Rwork0.339 1262 -
obs--68.17 %

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