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- PDB-6zij: Crystal Structure of Two-Domain Laccase mutant R240H from Strepto... -

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Basic information

Entry
Database: PDB / ID: 6zij
TitleCrystal Structure of Two-Domain Laccase mutant R240H 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: 1.6 Å
AuthorsGabdulkhakov, A.G. / Tishchenko, T.V. / Kolyadenko, I.A.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-04-00270 Russian Federation
Russian Foundation for Basic Research19-34-90121 Russian Federation
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2022
Title: The role of positive charged residue in the proton-transfer mechanism of two-domain laccase from Streptomyces griseoflavus Ac-993.
Authors: Gabdulkhakov, A. / Kolyadenko, I. / Oliveira, P. / Tamagnini, P. / Mikhaylina, A. / Tishchenko, S.
History
DepositionJun 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 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

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)210,77046
Polymers208,3966
Non-polymers2,37540
Water17,366964
1
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,41324
Polymers104,1983
Non-polymers1,21521
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12900 Å2
ΔGint-143 kcal/mol
Surface area27240 Å2
MethodPISA
2
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,35722
Polymers104,1983
Non-polymers1,15919
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12300 Å2
ΔGint-153 kcal/mol
Surface area27200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.040, 94.320, 116.830
Angle α, β, γ (deg.)90.000, 90.687, 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

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Two-domain laccase


Mass: 34732.590 Da / Num. of mol.: 6 / Mutation: R240H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseoflavus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4FJ81, laccase

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Non-polymers , 6 types, 1004 molecules

#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 964 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: 20 % w/v PEG 3350 0.2 M Ammonium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 207262 / % possible obs: 96.8 % / Redundancy: 3.34 % / Biso Wilson estimate: 19.94 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.34
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 15082 / CC1/2: 0.51

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PHENIX1.18_3861refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LHL

5lhl


Resolution: 1.6→45.83 Å / SU ML: 0.1824 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 20.2377
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1811 10124 4.88 %
Rwork0.1448 197124 -
obs0.1466 207248 96.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.98 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12742 0 77 964 13783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006613421
X-RAY DIFFRACTIONf_angle_d0.796118252
X-RAY DIFFRACTIONf_chiral_restr0.05651860
X-RAY DIFFRACTIONf_plane_restr0.00482450
X-RAY DIFFRACTIONf_dihedral_angle_d21.41814793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.33773380.27936370X-RAY DIFFRACTION95.11
1.62-1.640.31513540.24696518X-RAY DIFFRACTION96.48
1.64-1.660.29363280.23226514X-RAY DIFFRACTION96.33
1.66-1.680.30623370.23046536X-RAY DIFFRACTION96.38
1.68-1.70.30753130.22646523X-RAY DIFFRACTION96.43
1.7-1.720.28653270.21856576X-RAY DIFFRACTION96.67
1.72-1.750.26023710.2056534X-RAY DIFFRACTION96.61
1.75-1.770.2343210.19156413X-RAY DIFFRACTION95.54
1.77-1.80.24143620.18216239X-RAY DIFFRACTION92.88
1.8-1.830.22363390.17916558X-RAY DIFFRACTION96.48
1.83-1.860.2533410.18416497X-RAY DIFFRACTION96.69
1.86-1.90.23133180.17236572X-RAY DIFFRACTION96.69
1.9-1.930.21533100.16786592X-RAY DIFFRACTION96.8
1.93-1.970.21343470.15896575X-RAY DIFFRACTION96.73
1.97-2.020.20193530.14876482X-RAY DIFFRACTION96.24
2.02-2.060.20043130.14376503X-RAY DIFFRACTION96.26
2.06-2.110.19082910.146691X-RAY DIFFRACTION97.45
2.11-2.170.18513310.1436594X-RAY DIFFRACTION97.58
2.17-2.240.20183730.13996615X-RAY DIFFRACTION97.86
2.24-2.310.1963770.14276595X-RAY DIFFRACTION98.02
2.31-2.390.18673080.13826692X-RAY DIFFRACTION98.05
2.39-2.490.17953900.1386587X-RAY DIFFRACTION97.83
2.49-2.60.18493150.13716737X-RAY DIFFRACTION98.44
2.6-2.740.17042980.14026735X-RAY DIFFRACTION98.34
2.74-2.910.18412870.1446723X-RAY DIFFRACTION98.41
2.91-3.130.17053330.14036648X-RAY DIFFRACTION97.2
3.13-3.450.1623490.13666627X-RAY DIFFRACTION97.47
3.45-3.950.14443920.1256564X-RAY DIFFRACTION96.6
3.95-4.970.11873580.10516662X-RAY DIFFRACTION97.64
4.97-45.830.14623500.13286652X-RAY DIFFRACTION95.66

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