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- PDB-6evg: Structural and Functional Characterisation of a Bacterial Laccase... -

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Basic information

Entry
Database: PDB / ID: 6evg
TitleStructural and Functional Characterisation of a Bacterial Laccase-like Multi-copper Oxidase CueO from Lignin-Degrading Bacterium Ochrobactrum sp. with Oxidase Activity towards Lignin Model Compounds and Lignosulfonate
ComponentsMulti-copper Oxidase CueO
KeywordsOXIDOREDUCTASE / Laccase / Ochrobactrum / lignin degradation / copper protein
Function / homology
Function and homology information


cuproxidase / oxidoreductase activity / copper ion binding
Similarity search - Function
Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins ...Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Multicopper oxidase CueO
Similarity search - Component
Biological speciesOchrobactrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsFulop, V. / Wilkinson, R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M025772/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M003523/1 United Kingdom
CitationJournal: FEBS J. / Year: 2018
Title: Structural and functional characterisation of multi-copper oxidase CueO from lignin-degrading bacterium Ochrobactrum sp. reveal its activity towards lignin model compounds and lignosulfonate.
Authors: Granja-Travez, R.S. / Wilkinson, R.C. / Persinoti, G.F. / Squina, F.M. / Fulop, V. / Bugg, T.D.H.
History
DepositionNov 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_volume ..._chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multi-copper Oxidase CueO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3234
Polymers55,1351
Non-polymers1883
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint8 kcal/mol
Surface area17110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.330, 48.310, 88.850
Angle α, β, γ (deg.)90.00, 93.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Multi-copper Oxidase CueO


Mass: 55135.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochrobactrum (bacteria) / Plasmid: pET151 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6X5N0*PLUS, laccase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 1.84 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M MIB buffer pH 8, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 20, 2017
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.1→89 Å / Num. obs: 161992 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.72 % / Biso Wilson estimate: 9.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.2
Reflection shellResolution: 1.1→1.16 Å / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 11395 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX5.8.0171refinement
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PAV

3pav


Resolution: 1.1→88.66 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.95 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14926 6517 4 %RANDOM
Rwork0.1254 ---
obs0.12636 155475 99.87 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso mean: 14.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20.05 Å2
2--0.28 Å20 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.1→88.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3433 0 9 475 3917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193522
X-RAY DIFFRACTIONr_bond_other_d0.0020.023276
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.964771
X-RAY DIFFRACTIONr_angle_other_deg1.05437599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5975442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02823.951162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.69415579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7791524
X-RAY DIFFRACTIONr_chiral_restr0.1310.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213947
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02701
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_it1.1761.141774
X-RAY DIFFRACTIONr_mcbond_other1.1731.141773
X-RAY DIFFRACTIONr_mcangle_it1.5271.7252214
X-RAY DIFFRACTIONr_mcangle_other1.5281.7252215
X-RAY DIFFRACTIONr_scbond_it1.8691.4121748
X-RAY DIFFRACTIONr_scbond_other1.8691.4121748
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2572.0072558
X-RAY DIFFRACTIONr_long_range_B_refined3.07815.3273714
X-RAY DIFFRACTIONr_long_range_B_other2.62614.453593
X-RAY DIFFRACTIONr_rigid_bond_restr3.40936798
X-RAY DIFFRACTIONr_sphericity_free21.6685328
X-RAY DIFFRACTIONr_sphericity_bonded7.70756866
LS refinement shellResolution: 1.1→1.129 Å
RfactorNum. reflection% reflection
Rfree0.246 493 -
Rwork0.242 11395 -
obs--99.51 %

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