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- PDB-8paq: Structure of the small subunit of the laccase-like Nlac protein f... -

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Basic information

Entry
Database: PDB / ID: 8paq
TitleStructure of the small subunit of the laccase-like Nlac protein from Pleurotus eryngii
ComponentsPOXA3b laccase small subunit
KeywordsOXIDOREDUCTASE / NLac / PeNL / Pleurotus eryngii / Small subunit / Laccase-like enzyme
Function / homologyhydroquinone:oxygen oxidoreductase activity / laccase / IMIDAZOLE / POXA3b laccase small subunit
Function and homology information
Biological speciesPleurotus eryngii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMedrano, F.J. / Camarero, S.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)BIO2017-86559-R Spain
Ministerio de Ciencia e Innovacion (MCIN)PID2021-126384OB-I00 Spain
CitationJournal: Protein Sci. / Year: 2023
Title: Role and structure of the small subunit forming heterodimers with laccase-like enzymes.
Authors: Aza, P. / Linde, D. / Molpeceres, G. / Vind, J. / Medrano, F.J. / Camarero, S.
History
DepositionJun 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POXA3b laccase small subunit
B: POXA3b laccase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2298
Polymers34,8512
Non-polymers3786
Water5,675315
1
A: POXA3b laccase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6665
Polymers17,4251
Non-polymers2404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: POXA3b laccase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5643
Polymers17,4251
Non-polymers1382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.720, 124.720, 55.812
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein POXA3b laccase small subunit


Mass: 17425.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pleurotus eryngii (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6G7BM61, laccase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.11 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Imidazole at pH 8.0 and 2.5 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 1.6→47.16 Å / Num. obs: 58835 / % possible obs: 99.9 % / Redundancy: 26.2 % / Biso Wilson estimate: 25.78 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.29
Reflection shellResolution: 1.6→1.69 Å / Mean I/σ(I) obs: 0.69 / Num. unique obs: 9324 / CC1/2: 0.385 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→47.16 Å / SU ML: 0.2378 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.2677
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2191 1996 3.4 %
Rwork0.1941 56717 -
obs0.1949 58713 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.88 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 25 315 2677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592390
X-RAY DIFFRACTIONf_angle_d0.77963265
X-RAY DIFFRACTIONf_chiral_restr0.0453421
X-RAY DIFFRACTIONf_plane_restr0.0057427
X-RAY DIFFRACTIONf_dihedral_angle_d4.8441332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.42091350.41143831X-RAY DIFFRACTION95.89
1.64-1.680.34491400.33533989X-RAY DIFFRACTION99.83
1.68-1.730.3561420.32244026X-RAY DIFFRACTION99.95
1.73-1.790.27461410.28213997X-RAY DIFFRACTION99.9
1.79-1.850.30991400.2674001X-RAY DIFFRACTION100
1.85-1.920.29071430.25744059X-RAY DIFFRACTION99.95
1.92-2.010.25461410.24484004X-RAY DIFFRACTION100
2.01-2.120.22821410.20124014X-RAY DIFFRACTION100
2.12-2.250.22691430.18984047X-RAY DIFFRACTION100
2.25-2.420.22031430.18784072X-RAY DIFFRACTION100
2.42-2.670.24171440.19134073X-RAY DIFFRACTION100
2.67-3.050.19261440.17954101X-RAY DIFFRACTION100
3.05-3.850.16561450.16314152X-RAY DIFFRACTION100
3.85-47.160.20091540.16544351X-RAY DIFFRACTION99.91

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