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

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Basic information

Entry
Database: PDB / ID: 9rck
TitleLaccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant M455A-M456A soaked with Copper 2 minutes
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 4618 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 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
C: Multicopper oxidase domain-containing protein
A: Multicopper oxidase domain-containing protein
B: Multicopper oxidase domain-containing protein
E: Multicopper oxidase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,36426
Polymers238,9334
Non-polymers1,43122
Water4,252236
1
C: Multicopper oxidase domain-containing protein
B: Multicopper oxidase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,19813
Polymers119,4672
Non-polymers73211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-137 kcal/mol
Surface area17510 Å2
2
A: Multicopper oxidase domain-containing protein
E: Multicopper oxidase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,16613
Polymers119,4672
Non-polymers69911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-122 kcal/mol
Surface area17340 Å2
Unit cell
Length a, b, c (Å)123.115, 123.115, 179.736
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: 59733.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediococcus pentosaceus 4618 (bacteria)
Strain: 4618 / Gene: ITQ90_10235 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0AB73HHR8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 85% 1 M Ammonium Sulfate, 0.1 M Sodium Acetate pH 4.6 and 15% of another condition with 0.2 Sodium Chloride, 0.1 M Phosphate-citrate pH 4.2 and 20% PEG 8000

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Data collection

DiffractionMean temperature: 180 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.37723 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37723 Å / Relative weight: 1
ReflectionResolution: 2.3→52.29 Å / Num. obs: 70560 / % possible obs: 100 % / Redundancy: 19.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.038 / Rrim(I) all: 0.169 / Χ2: 0.98 / Net I/σ(I): 14.2
Reflection shellResolution: 2.3→2.35 Å / % possible obs: 100 % / Redundancy: 19.9 % / Rmerge(I) obs: 2.162 / Num. measured all: 88740 / Num. unique obs: 4450 / CC1/2: 0.829 / Rpim(I) all: 0.492 / Rrim(I) all: 2.218 / Χ2: 0.98 / 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: 2.3→52.29 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.402 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21705 3443 4.9 %RANDOM
Rwork0.18788 ---
obs0.18925 67048 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.521 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.42 Å20 Å2
2--0.83 Å2-0 Å2
3----2.7 Å2
Refinement stepCycle: 1 / Resolution: 2.3→52.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7322 0 26 236 7584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0127574
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166768
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.82110376
X-RAY DIFFRACTIONr_angle_other_deg0.4491.7515625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2995930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.921536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.735101075
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.21120
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021708
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_it2.3324.4793729
X-RAY DIFFRACTIONr_mcbond_other2.334.4793729
X-RAY DIFFRACTIONr_mcangle_it3.5548.0384656
X-RAY DIFFRACTIONr_mcangle_other3.5558.0394657
X-RAY DIFFRACTIONr_scbond_it2.9344.7873845
X-RAY DIFFRACTIONr_scbond_other2.9344.7883846
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7558.645721
X-RAY DIFFRACTIONr_long_range_B_refined6.63143.497708
X-RAY DIFFRACTIONr_long_range_B_other6.6343.47702
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 288 -
Rwork0.273 4854 -
obs--99.86 %

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