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- PDB-8p9v: Crystal Structure of Two-Domain Laccase mutant M199G/R240H/D268N ... -

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Basic information

Entry
Database: PDB / ID: 8p9v
TitleCrystal Structure of Two-Domain Laccase mutant M199G/R240H/D268N from Streptomyces griseoflavus
ComponentsTwo-domain laccase
KeywordsOXIDOREDUCTASE / Two-domain laccase / enzyme engineering / SgfSL / TNC / proton transport / laccase trinuclear cluster / oxygen reduction / structural biology
Function / homology
Function and homology information


hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding
Similarity search - Function
Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase / Multicopper oxidase, C-terminal / 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 / OXYGEN MOLECULE / PEROXIDE ION / Two-domain laccase
Similarity search - Component
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKolyadenko, I.A. / Tishchenko, S.V. / Gabdulkhakov, A.G.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation Russian Federation
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structural Insight into the Amino Acid Environment of the Two-Domain Laccase's Trinuclear Copper Cluster.
Authors: Kolyadenko, I. / Tishchenko, S. / Gabdulkhakov, A.
History
DepositionJun 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,85235
Polymers181,1676
Non-polymers1,68529
Water2,288127
1
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,41017
Polymers90,5843
Non-polymers82714
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11560 Å2
ΔGint-152 kcal/mol
Surface area27510 Å2
MethodPISA
2
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,44218
Polymers90,5843
Non-polymers85915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11850 Å2
ΔGint-152 kcal/mol
Surface area27500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.370, 93.920, 119.591
Angle α, β, γ (deg.)90.000, 91.100, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Two-domain laccase


Mass: 30194.531 Da / Num. of mol.: 6 / Mutation: M199G/R240H/D268N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseoflavus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4FJ81, laccase
#2: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 5
Details: 15 % v/v PEG Smear High, 0.15 M Ammonium acetate, 0.1 M Sodium citrate condition #31 of BCS-1 from Molecular Dimensions, UK

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→23.76 Å / Num. obs: 82258 / % possible obs: 98.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 17.8 Å2 / CC1/2: 0.96 / Net I/σ(I): 4.89
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.35 / Num. unique obs: 8233 / CC1/2: 0.49 / % possible all: 96.66

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASER2.8.2 (svn 8338)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→23.76 Å / SU ML: 0.3074 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.2021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.258 4124 5.03 %
Rwork0.215 77941 -
obs0.2171 82065 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.69 Å2
Refinement stepCycle: LAST / Resolution: 2.2→23.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12695 0 34 127 12856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008913154
X-RAY DIFFRACTIONf_angle_d0.98917887
X-RAY DIFFRACTIONf_chiral_restr0.05881828
X-RAY DIFFRACTIONf_plane_restr0.00932397
X-RAY DIFFRACTIONf_dihedral_angle_d16.24354660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.32591390.27112593X-RAY DIFFRACTION95.79
2.23-2.250.30311110.27662686X-RAY DIFFRACTION97.25
2.25-2.280.33271230.26972635X-RAY DIFFRACTION96.91
2.28-2.310.33761210.282688X-RAY DIFFRACTION97.87
2.31-2.340.3191380.27332672X-RAY DIFFRACTION97.03
2.34-2.380.33451270.26472672X-RAY DIFFRACTION98.21
2.38-2.410.25641440.26182637X-RAY DIFFRACTION97.2
2.41-2.450.32841680.27362650X-RAY DIFFRACTION97.98
2.45-2.490.30391690.26792648X-RAY DIFFRACTION97.81
2.49-2.530.31431220.2652653X-RAY DIFFRACTION97.64
2.53-2.580.28361410.25142698X-RAY DIFFRACTION98.75
2.58-2.630.29181650.2582629X-RAY DIFFRACTION97.9
2.63-2.680.31451570.25492657X-RAY DIFFRACTION97.88
2.68-2.740.32671530.26332691X-RAY DIFFRACTION98.89
2.74-2.80.30951380.24882675X-RAY DIFFRACTION98.32
2.8-2.870.28531470.25732670X-RAY DIFFRACTION98.26
2.87-2.950.30611520.27582660X-RAY DIFFRACTION97.88
2.95-3.040.34141460.2692686X-RAY DIFFRACTION98.13
3.04-3.140.33361700.24442664X-RAY DIFFRACTION98.57
3.14-3.250.23961460.22152735X-RAY DIFFRACTION99.04
3.25-3.380.23731180.20472721X-RAY DIFFRACTION99.47
3.38-3.530.20391240.18152740X-RAY DIFFRACTION99.51
3.53-3.720.22961400.17742740X-RAY DIFFRACTION99.52
3.72-3.950.24171580.18372688X-RAY DIFFRACTION99.41
3.95-4.250.16891480.16392752X-RAY DIFFRACTION99.72
4.25-4.680.18421160.14212759X-RAY DIFFRACTION99.24
4.68-5.350.19491470.14682737X-RAY DIFFRACTION99.48
5.35-6.710.191490.16422767X-RAY DIFFRACTION99.52
6.71-23.760.20221470.17262738X-RAY DIFFRACTION97.14

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