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- PDB-9f1t: Psychrophilic laccase (multicopper oxidase) from Oenococcus oeni ... -

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Basic information

Entry
Database: PDB / ID: 9f1t
TitlePsychrophilic laccase (multicopper oxidase) from Oenococcus oeni 229 without Histag
ComponentsMulticopper oxidase
KeywordsOXIDOREDUCTASE / Laccase / oxidorreductase / multicopper oxidase
Function / homology
Function and homology information


oxidoreductase activity / copper ion binding
Similarity search - Function
Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / 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
Similarity search - Component
Biological speciesOenococcus oeni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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: Int J Mol Sci / Year: 2024
Title: Biochemical and Structural Characterization of a Novel Psychrophilic Laccase (Multicopper Oxidase) Discovered from Oenococcus oeni 229 (ENOLAB 4002).
Authors: Olmeda, I. / Paredes-Martinez, F. / Sendra, R. / Casino, P. / Pardo, I. / Ferrer, S.
History
DepositionApr 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI
Revision 1.2Aug 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Multicopper oxidase
A: Multicopper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,69210
Polymers111,1842
Non-polymers5088
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-56 kcal/mol
Surface area33790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.672, 97.865, 96.098
Angle α, β, γ (deg.)90.00, 91.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Multicopper oxidase


Mass: 55591.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oenococcus oeni (bacteria) / Gene: OEOE_0009 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q04HQ8
#2: Chemical
ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.2289659 Å3/Da / Density % sol: 44.84415 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 18% PEG 10000, 20% glycerol, 100 mM Tris-HCl pH 8.5 and 100 mM NaCl

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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: Mar 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3→68.65 Å / Num. obs: 19139 / % possible obs: 97.8 % / Redundancy: 4.7 % / CC1/2: 0.912 / Rmerge(I) obs: 0.299 / Rpim(I) all: 0.15 / Rrim(I) all: 0.336 / Χ2: 0.85 / Net I/σ(I): 4.4
Reflection shellResolution: 3→3.18 Å / % possible obs: 97.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.788 / Num. measured all: 14384 / Num. unique obs: 3066 / CC1/2: 0.66 / Rpim(I) all: 0.401 / Rrim(I) all: 0.889 / Χ2: 0.92 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→68.65 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.831 / SU B: 27.52 / SU ML: 0.487 / Cross valid method: THROUGHOUT / ESU R Free: 0.524 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26629 847 4.4 %RANDOM
Rwork0.21929 ---
obs0.22139 18254 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.207 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å20 Å2-0.21 Å2
2---3.46 Å2-0 Å2
3---6.03 Å2
Refinement stepCycle: 1 / Resolution: 3→68.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7405 0 8 74 7487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0127607
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167011
X-RAY DIFFRACTIONr_angle_refined_deg1.1321.80610389
X-RAY DIFFRACTIONr_angle_other_deg0.4681.75116138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4585951
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.276538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.457101159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0480.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029063
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021705
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_it0.7272.053810
X-RAY DIFFRACTIONr_mcbond_other0.7272.053810
X-RAY DIFFRACTIONr_mcangle_it1.2663.6784759
X-RAY DIFFRACTIONr_mcangle_other1.2663.6784760
X-RAY DIFFRACTIONr_scbond_it0.9252.1063797
X-RAY DIFFRACTIONr_scbond_other0.9252.1063798
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5533.8315631
X-RAY DIFFRACTIONr_long_range_B_refined3.93624.5530802
X-RAY DIFFRACTIONr_long_range_B_other3.93524.5530791
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 63 -
Rwork0.317 1342 -
obs--97.3 %

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