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- PDB-9rc8: Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 d... -

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Basic information

Entry
Database: PDB / ID: 9rc8
TitleLaccase (multicopper oxidase) from Pediococcus pentosaceus 4618 deletion 482-509 co-crystallized with Copper Chloride
ComponentsMulticopper oxidase domain-containing protein
KeywordsOXIDOREDUCTASE / Laccase / multicopper oxidase
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciesPediococcus pentosaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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
Citation
Journal: Protein Sci. / Year: 2026
Title: Laccases from lactic acid bacteria show cuprous oxidase activity and capture Cu(II) and Ag(I) ions.
Authors: Gasco, R. / Sendra, R. / Olmeda, I. / Paredes-Martinez, F. / Ferrer, S. / Pardo, I. / Casino, P.
#1: Journal: 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
Revision 1.1Jan 14, 2026Group: Database references / Category: citation / citation_author

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,62910
Polymers113,1212
Non-polymers5088
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-84 kcal/mol
Surface area32730 Å2
Unit cell
Length a, b, c (Å)124.363, 124.363, 182.238
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: 56560.473 Da / Num. of mol.: 2
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)
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 2M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 180 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97895 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 3.2→107.7 Å / Num. obs: 27532 / % possible obs: 100 % / Redundancy: 9.5 % / CC1/2: 0.988 / Rmerge(I) obs: 0.299 / Rpim(I) all: 0.102 / Rrim(I) all: 0.316 / Χ2: 1 / Net I/σ(I): 8.9 / Num. measured all: 261394
Reflection shellResolution: 3.2→3.39 Å / % possible obs: 100 % / Redundancy: 9.7 % / Rmerge(I) obs: 1.137 / Num. measured all: 42362 / Num. unique obs: 4387 / CC1/2: 0.813 / Rpim(I) all: 0.384 / Rrim(I) all: 1.2 / Χ2: 1.04 / Net I/σ(I) obs: 2.6

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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: 3.2→107.7 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / SU B: 16.539 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20979 1359 4.9 %RANDOM
Rwork0.15936 ---
obs0.1619 26136 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: 56.676 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20.38 Å2-0 Å2
2--0.76 Å2-0 Å2
3----2.45 Å2
Refinement stepCycle: 1 / Resolution: 3.2→107.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7288 0 8 81 7377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0127522
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166745
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.82310297
X-RAY DIFFRACTIONr_angle_other_deg0.4341.7515579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2925922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.254536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.881101095
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0570.21107
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028928
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021700
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_it2.9945.6583694
X-RAY DIFFRACTIONr_mcbond_other2.995.6583694
X-RAY DIFFRACTIONr_mcangle_it4.8610.1674614
X-RAY DIFFRACTIONr_mcangle_other4.8610.1684615
X-RAY DIFFRACTIONr_scbond_it3.4315.9473828
X-RAY DIFFRACTIONr_scbond_other3.435.9483829
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.67710.7775684
X-RAY DIFFRACTIONr_long_range_B_refined8.30653.27713
X-RAY DIFFRACTIONr_long_range_B_other8.30653.237706
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 104 -
Rwork0.265 1901 -
obs--99.95 %

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