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- PDB-6ryx: Copper oxidase from Colletotrichum graminicola -

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Basic information

Entry
Database: PDB / ID: 6ryx
TitleCopper oxidase from Colletotrichum graminicola
ComponentsKelch domain-containing protein
KeywordsOXIDOREDUCTASE / Copper radical oxidase / 5-hydroxymethylfurfural / auxiliary activity / aryl-alcohol oxidase
Function / homology
Function and homology information


Galactose oxidase-like, Early set domain / Galactose oxidase, central domain superfamily / Galactose oxidase-like, Early set domain / Kelch motif / Galactose oxidase/kelch, beta-propeller / PAN domain / PAN/Apple domain / Kelch / Kelch motif / Kelch repeat type 1 ...Galactose oxidase-like, Early set domain / Galactose oxidase, central domain superfamily / Galactose oxidase-like, Early set domain / Kelch motif / Galactose oxidase/kelch, beta-propeller / PAN domain / PAN/Apple domain / Kelch / Kelch motif / Kelch repeat type 1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
COPPER (II) ION / DI(HYDROXYETHYL)ETHER / Kelch domain-containing protein
Similarity search - Component
Biological speciesColletotrichum graminicola
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsOffen, W.A. / Henrissat, B. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal SocietyRP150126 United Kingdom
CitationJournal: Acs Catalysis / Year: 2020
Title: Discovery of a Fungal Copper Radical Oxidase with High Catalytic Efficiency toward 5-Hydroxymethylfurfural and Benzyl Alcohols for Bioprocessing
Authors: Mathieu, Y. / Offen, W.A. / Forget, S.M. / Ciano, L. / Viborg, A.H. / Blagova, E. / Walton, P.H. / Davies, G.J. / Brumer, H.
History
DepositionJun 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: chem_comp / pdbx_validate_close_contact ...chem_comp / pdbx_validate_close_contact / refine / struct_conn
Item: _chem_comp.type / _refine.details
Revision 1.2Apr 8, 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.title / _citation.year / _citation_author.name
Revision 1.3May 27, 2020Group: Structure summary / Category: audit_author
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.pdbx_value_order / _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.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 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 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kelch domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9894
Polymers77,5981
Non-polymers3913
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-7 kcal/mol
Surface area22940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.043, 172.043, 172.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Kelch domain-containing protein


Mass: 77597.984 Da / Num. of mol.: 1 / Mutation: Y336W
Source method: isolated from a genetically manipulated source
Details: Secreted part of oxidase after cloning without signal sequence and after adding alpha-factor secretion signal for expression in Pichia pastoris; C-terminus has His tag. Mutated at Y334 to W
Source: (gene. exp.) Colletotrichum graminicola (strain M1.001 / M2 / FGSC 10212) (fungus)
Strain: M1.001 / M2 / FGSC 10212 / Gene: GLRG_02805 / Variant: M1.001 / M2 / FGSC 10212 / Production host: Komagataella pastoris (fungus) / References: UniProt: E3Q9X3, aryl-alcohol oxidase
#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.: 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
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG 4000, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.65→121.65 Å / Num. obs: 24743 / % possible obs: 100 % / Redundancy: 24.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.045 / Net I/σ(I): 12
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 23.3 % / Num. unique obs: 3283 / CC1/2: 0.535 / Rpim(I) all: 0.581 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C86

5c86


Resolution: 2.65→121.65 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.895 / SU B: 13.612 / SU ML: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.575 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THERE IS A TYROSYL-CYSTEINE THIOETHER BOND BETWEEN CYS272 AND TYR316
RfactorNum. reflection% reflectionSelection details
Rfree0.2797 1228 5 %RANDOM
Rwork0.221 ---
obs0.2241 23451 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.8 Å2 / Biso mean: 51.754 Å2 / Biso min: 23.23 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.65→121.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4567 0 22 11 4600
Biso mean--71.35 49.31 -
Num. residues----626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134729
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174010
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.6486468
X-RAY DIFFRACTIONr_angle_other_deg1.2461.5779281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3185624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89722.67221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.23615616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7611523
X-RAY DIFFRACTIONr_chiral_restr0.0610.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025511
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021012
LS refinement shellResolution: 2.651→2.72 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 95 -
Rwork0.296 1707 -
all-1802 -
obs--100 %

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