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

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Basic information

Entry
Database: PDB / ID: 9rcn
TitleLaccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant E451L co-crystallized with Silver Nitrate (2 molecules in assymetric unit)
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
SILVER ION / COPPER (II) ION / Multicopper oxidase domain-containing protein
Similarity search - Component
Biological speciesPediococcus pentosaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)PID2022-14161NB-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 29, 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)180,63317
Polymers179,5133
Non-polymers1,12014
Water88349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-151 kcal/mol
Surface area33550 Å2
Unit cell
Length a, b, c (Å)119.807, 119.807, 174.255
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: 59837.562 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 25% PEG4000 Sodium Citrate pH 5.6 0.2M Ammonium Sulphate

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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 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.5→103.76 Å / Num. obs: 50079 / % possible obs: 99.2 % / Redundancy: 12.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.041 / Rrim(I) all: 0.145 / Χ2: 1.01 / Net I/σ(I): 13.6 / Num. measured all: 623633
Reflection shellResolution: 2.5→2.58 Å / % possible obs: 98.6 % / Redundancy: 13 % / Rmerge(I) obs: 1.357 / Num. measured all: 58631 / Num. unique obs: 4523 / CC1/2: 0.765 / Rpim(I) all: 0.388 / Rrim(I) all: 1.412 / Χ2: 1.03 / Net I/σ(I) obs: 2.2

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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: 2.5→103.76 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.472 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21833 2536 5.1 %RANDOM
Rwork0.17944 ---
obs0.18149 47536 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.591 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.28 Å20 Å2
2--0.55 Å2-0 Å2
3----1.79 Å2
Refinement stepCycle: 1 / Resolution: 2.5→103.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7382 0 26 49 7457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0127633
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166856
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.82610442
X-RAY DIFFRACTIONr_angle_other_deg0.4531.75615843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2255929
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.369536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.038101129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.21124
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028998
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021714
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_it3.3425.4333725
X-RAY DIFFRACTIONr_mcbond_other3.3425.4333725
X-RAY DIFFRACTIONr_mcangle_it4.9079.7614651
X-RAY DIFFRACTIONr_mcangle_other4.9079.7614652
X-RAY DIFFRACTIONr_scbond_it4.0855.833908
X-RAY DIFFRACTIONr_scbond_other4.0855.833909
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.45210.5135792
X-RAY DIFFRACTIONr_long_range_B_refined8.44851.787712
X-RAY DIFFRACTIONr_long_range_B_other8.44851.787713
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 174 -
Rwork0.297 3436 -
obs--98.34 %

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