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Structural 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
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PAV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 0.1 M MIB buffer pH 8, 25% PEG 1500
Crystal Properties Matthews coefficient Solvent content 1.84 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.33 α = 90 b = 48.31 β = 93.78 c = 88.85 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2017-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.8 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.1 89 99.9 0.056 0.999 12.2 3.72 161992 -3 9.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.16 99.7 0.584 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3PAV 1.1 88.66 155475 6517 99.87 0.12636 0.1254 0.1384 0.14926 0.1584 RANDOM 14.14
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.18 0.05 0.28 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.028 r_sphericity_free 21.668 r_dihedral_angle_4_deg 20.779 r_dihedral_angle_3_deg 10.694 r_sphericity_bonded 7.707 r_dihedral_angle_1_deg 6.597 r_rigid_bond_restr 3.409 r_long_range_B_refined 3.078 r_long_range_B_other 2.626 r_scangle_other 2.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.028 r_sphericity_free 21.668 r_dihedral_angle_4_deg 20.779 r_dihedral_angle_3_deg 10.694 r_sphericity_bonded 7.707 r_dihedral_angle_1_deg 6.597 r_rigid_bond_restr 3.409 r_long_range_B_refined 3.078 r_long_range_B_other 2.626 r_scangle_other 2.257 r_scbond_it 1.869 r_scbond_other 1.869 r_angle_refined_deg 1.862 r_mcangle_other 1.528 r_mcangle_it 1.527 r_mcbond_it 1.176 r_mcbond_other 1.173 r_angle_other_deg 1.054 r_chiral_restr 0.131 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3433 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling BALBES phasing