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- PDB-9rc6: Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 m... -

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Basic information

Entry
Database: PDB / ID: 9rc6
TitleLaccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant Y471L co-crystallized with Copper Chloride
ComponentsMulticopper oxidase domain-containing protein
KeywordsOXIDOREDUCTASE / Laccase / multicopper oxidase
Function / homology
Function and homology information


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, N-terminal / Multicopper oxidase / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / Multicopper oxidase domain-containing protein
Similarity search - Component
Biological speciesPediococcus pentosaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsParedes, F. / Casino, P.
Funding support Spain, 3items
OrganizationGrant numberCountry
Generalitat ValencianaCIAICO/2022/142 Spain
Ministerio de Ciencia e Innovacion (MCIN)PID2019-110630GB-I00 Spain
Ministerio de Ciencia e Innovacion (MCIN)PID2022-141621NB-I00 Spain
CitationJournal: Protein Sci. / Year: 2025
Title: Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 co-crystallized with Silver Nitrate
Authors: Gasco, R. / Sendra, R. / Olmeda, I. / Paredes, F. / Ferrer, S. / Pardo, I. / Casino, P.
History
DepositionMay 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multicopper oxidase domain-containing protein
C: Multicopper oxidase domain-containing protein
G: Multicopper oxidase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,56119
Polymers179,2843
Non-polymers1,27716
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-194 kcal/mol
Surface area33550 Å2
Unit cell
Length a, b, c (Å)123.680, 123.680, 181.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Multicopper oxidase domain-containing protein


Mass: 59761.430 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediococcus pentosaceus (bacteria) / Strain: 4618 / Gene: ITQ90_10235 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0AB73HHR8
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5 M Ammonium Sulfate, 1 M Lithium Sulfate and 100 mM Sodium Citrate pH 5.6

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Data collection

DiffractionMean temperature: 180 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.6→107.11 Å / Num. obs: 50107 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.039 / Rrim(I) all: 0.123 / Χ2: 1.01 / Net I/σ(I): 13.8 / Num. measured all: 502327
Reflection shellResolution: 2.6→2.69 Å / % possible obs: 100 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.987 / Num. measured all: 41849 / Num. unique obs: 4582 / CC1/2: 0.829 / Rpim(I) all: 0.344 / Rrim(I) all: 1.046 / Χ2: 0.99 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→107.11 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.989 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22864 2472 4.9 %RANDOM
Rwork0.18934 ---
obs0.19128 47589 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 mean: 55.565 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20.5 Å20 Å2
2--0.99 Å2-0 Å2
3----3.22 Å2
Refinement stepCycle: 1 / Resolution: 2.6→107.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7363 0 48 64 7475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0127649
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166840
X-RAY DIFFRACTIONr_angle_refined_deg1.291.82510468
X-RAY DIFFRACTIONr_angle_other_deg0.481.75715809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6835930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.198536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.546101129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.21124
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029026
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021718
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_it3.25.5023723
X-RAY DIFFRACTIONr_mcbond_other3.1995.5023723
X-RAY DIFFRACTIONr_mcangle_it4.7849.8814652
X-RAY DIFFRACTIONr_mcangle_other4.7859.8824653
X-RAY DIFFRACTIONr_scbond_it3.6285.8083926
X-RAY DIFFRACTIONr_scbond_other3.6285.8093927
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.63810.5175817
X-RAY DIFFRACTIONr_long_range_B_refined7.70452.327779
X-RAY DIFFRACTIONr_long_range_B_other7.70352.327780
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 179 -
Rwork0.319 3447 -
obs--100 %

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