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- PDB-7pes: Crystal Structure of Two-Domain Laccase mutant M199G from Strepto... -

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Basic information

Entry
Database: PDB / ID: 7pes
TitleCrystal Structure of Two-Domain Laccase mutant M199G from Streptomyces griseoflavus
ComponentsTwo-domain laccase
KeywordsOXIDOREDUCTASE / Two-Domain Laccase / laccase / Streptomyces griseoflavus
Function / homology
Function and homology information


hydroquinone:oxygen oxidoreductase activity / laccase / iron ion transport / copper ion binding / plasma membrane
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 / OXYGEN MOLECULE / Two-domain laccase
Similarity search - Component
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGabdulkhakov, A. / Tishchenko, S. / Kolyadenko, I.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research19-34-90121 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2021
Title: Engineering the Catalytic Properties of Two-Domain Laccase from Streptomyces griseoflavus Ac-993.
Authors: Kolyadenko, I. / Scherbakova, A. / Kovalev, K. / Gabdulkhakov, A. / Tishchenko, S.
History
DepositionAug 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)186,59636
Polymers184,9156
Non-polymers1,68130
Water15,277848
1
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,29818
Polymers92,4583
Non-polymers84115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11830 Å2
ΔGint-158 kcal/mol
Surface area27440 Å2
MethodPISA
2
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,29818
Polymers92,4583
Non-polymers84115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-161 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.175, 94.355, 119.795
Angle α, β, γ (deg.)90.000, 91.135, 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: 30819.178 Da / Num. of mol.: 6 / Mutation: M199G
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-CU / COPPER (II) ION


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


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 848 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 15 % v/v PEG Smear High, 0.15 M Ammonium acetate, 0.1 M Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.977175 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977175 Å / Relative weight: 1
ReflectionResolution: 1.75→48 Å / Num. obs: 168209 / % possible obs: 99.9 % / Redundancy: 6.83 % / Biso Wilson estimate: 34.5 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.066 / Net I/σ(I): 14.3
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.02 / Num. unique obs: 12404 / CC1/2: 0.502 / Rrim(I) all: 1.86 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LHL

5lhl


Resolution: 1.75→47.18 Å / SU ML: 0.2253 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.4629
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2013 1767 1.05 %
Rwork0.1658 166409 -
obs0.1661 168176 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.45 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12739 0 32 848 13619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007113424
X-RAY DIFFRACTIONf_angle_d0.901518277
X-RAY DIFFRACTIONf_chiral_restr0.06231866
X-RAY DIFFRACTIONf_plane_restr0.00732461
X-RAY DIFFRACTIONf_dihedral_angle_d6.04971887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.31711360.318112756X-RAY DIFFRACTION100
1.8-1.850.31131350.27312754X-RAY DIFFRACTION99.95
1.85-1.910.27931350.238712711X-RAY DIFFRACTION99.98
1.91-1.980.29861360.225512793X-RAY DIFFRACTION99.96
1.98-2.060.2431350.201612736X-RAY DIFFRACTION99.95
2.06-2.150.24471360.182512790X-RAY DIFFRACTION99.99
2.15-2.260.24311350.175412771X-RAY DIFFRACTION99.96
2.26-2.410.22291360.178212807X-RAY DIFFRACTION99.98
2.41-2.590.21231360.17512806X-RAY DIFFRACTION100
2.59-2.850.21831360.178812811X-RAY DIFFRACTION100
2.85-3.270.20961360.175712845X-RAY DIFFRACTION99.95
3.27-4.110.19711360.152112831X-RAY DIFFRACTION99.89
4.11-47.180.14721390.130712998X-RAY DIFFRACTION99.58

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