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- PDB-9rc3: Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 c... -

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Basic information

Entry
Database: PDB / ID: 9rc3
TitleLaccase (multicopper oxidase) from Pediococcus pentosaceus 4618 co-crystallized with Silver Nitrate
ComponentsMulticopper oxidase, type 2
KeywordsOXIDOREDUCTASE / Laccase / multicopper oxidase
Function / homologySILVER ION / COPPER (II) ION
Function and homology information
Biological speciesPediococcus pentosaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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: Laccases from lactic acid bacteria show cuprous oxidase activity and capture Cu(II) and Ag(I) ions
Authors: Paredes, F. / 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

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Assembly

Deposited unit
A: Multicopper oxidase, type 2
B: Multicopper oxidase, type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,62314
Polymers119,7072
Non-polymers91612
Water34219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-123 kcal/mol
Surface area33230 Å2
Unit cell
Length a, b, c (Å)121.122, 121.122, 174.556
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, type 2


Mass: 59853.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediococcus pentosaceus (bacteria) / Production host: Escherichia coli K-12 (bacteria) / References: Oxidoreductases
#2: Chemical
ChemComp-CU / COPPER (II) ION


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


Mass: 107.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ag
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 25% PEG 4000, 100 mM Sodium Citrate pH 5.6 and 0.2 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 180 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.7→174.56 Å / Num. obs: 41277 / % possible obs: 99.9 % / Redundancy: 18.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.059 / Rrim(I) all: 0.187 / Χ2: 0.99 / Net I/σ(I): 15.9
Reflection shellResolution: 2.7→2.81 Å / Redundancy: 12 % / Rmerge(I) obs: 1.137 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4547 / CC1/2: 0.717 / Rpim(I) all: 0.493 / Rrim(I) all: 1.243 / Χ2: 0.99 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→104.89 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.916 / SU B: 11.714 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.478 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24933 2004 4.9 %RANDOM
Rwork0.20152 ---
obs0.20381 39227 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.365 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0.18 Å2-0 Å2
2---0.36 Å20 Å2
3---1.18 Å2
Refinement stepCycle: 1 / Resolution: 2.7→104.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7303 0 20 19 7342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0127549
X-RAY DIFFRACTIONr_bond_other_d0.0020.0166792
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.82710330
X-RAY DIFFRACTIONr_angle_other_deg0.4451.75615701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.45922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.646536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.975101122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0570.21113
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028923
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021693
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_it3.1635.553688
X-RAY DIFFRACTIONr_mcbond_other3.1565.553688
X-RAY DIFFRACTIONr_mcangle_it4.7829.9734607
X-RAY DIFFRACTIONr_mcangle_other4.7829.9744608
X-RAY DIFFRACTIONr_scbond_it3.6225.8533861
X-RAY DIFFRACTIONr_scbond_other3.6085.8443854
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7310.5925711
X-RAY DIFFRACTIONr_long_range_B_refined7.64454.567567
X-RAY DIFFRACTIONr_long_range_B_other7.64454.567568
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 141 -
Rwork0.298 2805 -
obs--98.2 %

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