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- PDB-9kol: Crystal structure of a Ruthenium and Copper-substituted small laccase -

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Basic information

Entry
Database: PDB / ID: 9kol
TitleCrystal structure of a Ruthenium and Copper-substituted small laccase
ComponentsCopper oxidase
KeywordsOXIDOREDUCTASE / oxidase / small laccase / artificial metalloenzyme
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / RUTHENIUM ION / Copper oxidase
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYang, X. / Fan, S. / Liu, J. / Wu, W. / Chen, X. / Ji, W. / Li, S. / Xue, Y. / Sun, X. / Wang, M. ...Yang, X. / Fan, S. / Liu, J. / Wu, W. / Chen, X. / Ji, W. / Li, S. / Xue, Y. / Sun, X. / Wang, M. / Wu, F. / Yu, P. / Mao, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv / Year: 2025
Title: Remolding laccase for whole-cell and in vivo modulation of dopamine signal
Authors: Yang, X. / Fan, S. / Liu, J. / Wu, W. / Chen, X. / Ji, W. / Li, S. / Xue, Y. / Sun, X. / Wang, M. / Wu, F. / Yu, P. / Mao, L.
History
DepositionNov 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8434
Polymers30,6151
Non-polymers2283
Water5,008278
1
A: Copper oxidase
hetero molecules

A: Copper oxidase
hetero molecules

A: Copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,53012
Polymers91,8453
Non-polymers6849
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11630 Å2
ΔGint-87 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.441, 177.441, 177.441
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-774-

HOH

21A-778-

HOH

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Components

#1: Protein Copper oxidase / Ruthenium and Copper substituted oxidase


Mass: 30615.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Gene: SCO6712, SC4C6.22 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: Q9XAL8
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-RU / RUTHENIUM ION


Mass: 101.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ru / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 7.6 Å3/Da / Density % sol: 83.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.8 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.5, 2% v/v polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jan 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.1→30.91 Å / Num. obs: 55922 / % possible obs: 99.79 % / Redundancy: 43.1 % / Biso Wilson estimate: 38.98 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.191 / Net I/σ(I): 21
Reflection shellResolution: 2.1→30.91 Å / Rmerge(I) obs: 0.191 / Num. unique obs: 3836 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
REFMAC5.8.0419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CG8

3cg8


Resolution: 2.1→30.91 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.749 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18794 2825 5 %RANDOM
Rwork0.16856 ---
obs0.16951 53253 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.44 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.1→30.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2154 0 3 278 2435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122216
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161976
X-RAY DIFFRACTIONr_angle_refined_deg2.1851.8163007
X-RAY DIFFRACTIONr_angle_other_deg0.7581.7744558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1355278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.555516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3310336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022677
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02518
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_it3.973.9321115
X-RAY DIFFRACTIONr_mcbond_other3.9383.9331115
X-RAY DIFFRACTIONr_mcangle_it5.1397.0271392
X-RAY DIFFRACTIONr_mcangle_other5.1617.0291393
X-RAY DIFFRACTIONr_scbond_it5.3694.2971101
X-RAY DIFFRACTIONr_scbond_other5.3674.2971101
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3667.6351616
X-RAY DIFFRACTIONr_long_range_B_refined8.71349.579439
X-RAY DIFFRACTIONr_long_range_B_other8.58748.869175
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.152 Å
RfactorNum. reflection% reflection
Rfree0.241 209 -
Rwork0.1728 3836 -
obs--100 %

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