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- PDB-6zip: Crystal Structure of Two-Domain Laccase mutant R240A from Strepto... -

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Basic information

Entry
Database: PDB / ID: 6zip
TitleCrystal Structure of Two-Domain Laccase mutant R240A from Streptomyces griseoflavus
ComponentsTwo-domain laccase
KeywordsOXIDOREDUCTASE / Two-Domain Laccase / laccase / Streptomyces griseoflavus
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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
G: Two-domain laccase
H: Two-domain laccase
I: Two-domain laccase
J: Two-domain laccase
K: Two-domain laccase
L: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)419,44167
Polymers415,98612
Non-polymers3,45455
Water14,268792
1
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,97518
Polymers103,9973
Non-polymers97915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-155 kcal/mol
Surface area27380 Å2
MethodPISA
2
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,88317
Polymers103,9973
Non-polymers88714
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11450 Å2
ΔGint-149 kcal/mol
Surface area27800 Å2
MethodPISA
3
G: Two-domain laccase
H: Two-domain laccase
I: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,79116
Polymers103,9973
Non-polymers79513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-153 kcal/mol
Surface area27500 Å2
MethodPISA
4
J: Two-domain laccase
K: Two-domain laccase
L: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,79116
Polymers103,9973
Non-polymers79513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11290 Å2
ΔGint-150 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.873, 94.838, 116.106
Angle α, β, γ (deg.)90.212, 90.241, 91.456
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Two-domain laccase


Mass: 34665.523 Da / Num. of mol.: 12 / Mutation: R240A
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 , 5 types, 847 molecules

#2: Chemical...
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PER / PEROXIDE ION / Peroxide


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


Mass: 18.015 Da / Num. of mol.: 792 / 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: 2.03 Å3/Da / Density % sol: 39.53 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 9.3 / Details: 20 % v/v PEG Smear High 0.1 M Bicine, pH 9.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.861 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.861 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 200840 / % possible obs: 97.6 % / Redundancy: 2.67 % / Biso Wilson estimate: 35.33 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.09
Reflection shellResolution: 2.05→2.1 Å / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.28 / Num. unique obs: 14801 / CC1/2: 0.69 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PHENIX1.18_3861refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LHL

5lhl


Resolution: 2.05→47.4 Å / SU ML: 0.2382 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.6624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2081 10156 5.06 %
Rwork0.1881 190492 -
obs0.1891 200648 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.55 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25438 0 74 792 26304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009126400
X-RAY DIFFRACTIONf_angle_d1.008335899
X-RAY DIFFRACTIONf_chiral_restr0.06023681
X-RAY DIFFRACTIONf_plane_restr0.00644804
X-RAY DIFFRACTIONf_dihedral_angle_d20.84269392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.070.31973910.31716328X-RAY DIFFRACTION97.12
2.07-2.10.32094150.29976173X-RAY DIFFRACTION97.03
2.1-2.120.323490.29356292X-RAY DIFFRACTION97.03
2.12-2.150.29073590.27956353X-RAY DIFFRACTION97.05
2.15-2.180.31263380.27966234X-RAY DIFFRACTION96.69
2.18-2.210.3033850.27146344X-RAY DIFFRACTION97.24
2.21-2.240.30423640.26766277X-RAY DIFFRACTION97.49
2.24-2.270.28043790.25756288X-RAY DIFFRACTION97.33
2.27-2.310.30393360.25626353X-RAY DIFFRACTION97.51
2.31-2.350.273100.24646354X-RAY DIFFRACTION97.47
2.35-2.390.2573250.23596357X-RAY DIFFRACTION97.31
2.39-2.430.26783240.24196363X-RAY DIFFRACTION97.49
2.43-2.480.26034100.24126338X-RAY DIFFRACTION97.95
2.48-2.530.28043250.23356355X-RAY DIFFRACTION97.79
2.53-2.580.26443190.23246370X-RAY DIFFRACTION97.52
2.58-2.640.26283410.23216348X-RAY DIFFRACTION97.32
2.64-2.710.25592850.22766352X-RAY DIFFRACTION97.42
2.71-2.780.2493250.22226398X-RAY DIFFRACTION97.65
2.78-2.860.2352970.22036412X-RAY DIFFRACTION97.97
2.86-2.960.23513060.20826456X-RAY DIFFRACTION97.97
2.96-3.060.23533260.20176351X-RAY DIFFRACTION97.79
3.06-3.180.20933370.19486377X-RAY DIFFRACTION98.03
3.18-3.330.21233450.19216383X-RAY DIFFRACTION97.58
3.33-3.510.20223080.17796355X-RAY DIFFRACTION97.53
3.51-3.720.17923760.1686283X-RAY DIFFRACTION97.84
3.72-4.010.18213720.15786419X-RAY DIFFRACTION98.46
4.01-4.420.14353340.13416406X-RAY DIFFRACTION98.55
4.42-5.050.13322510.12286470X-RAY DIFFRACTION97.8
5.05-6.360.12692960.13386429X-RAY DIFFRACTION98.03
6.37-47.40.14733280.15196274X-RAY DIFFRACTION96.41

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