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- PDB-7pen: Crystal Structure of Two-Domain Laccase mutant Y230A from Strepto... -

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Basic information

Entry
Database: PDB / ID: 7pen
TitleCrystal Structure of Two-Domain Laccase mutant Y230A 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 / Two-domain laccase
Similarity search - Component
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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

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)209,52832
Polymers207,9576
Non-polymers1,57126
Water24,1221339
1
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,76416
Polymers103,9793
Non-polymers78613
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11380 Å2
ΔGint-155 kcal/mol
Surface area28260 Å2
MethodPISA
2
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,76416
Polymers103,9793
Non-polymers78613
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11380 Å2
ΔGint-155 kcal/mol
Surface area27670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.260, 94.980, 116.270
Angle α, β, γ (deg.)90.000, 91.667, 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: 34659.543 Da / Num. of mol.: 6 / Mutation: Y230A
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.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1339 / 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: 2.05 Å3/Da / Density % sol: 40.02 %
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: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 220573 / % possible obs: 99.9 % / Redundancy: 5.63 % / Biso Wilson estimate: 20.11 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.1 / Net I/σ(I): 10.93
Reflection shellResolution: 1.6→1.64 Å / Num. unique obs: 16337 / CC1/2: 0.68 / Rrim(I) all: 1.13 / % possible all: 99.9

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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: 1.6→47.1 Å / SU ML: 0.1986 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.3746
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1653 8823 4 %
Rwork0.1353 211735 -
obs0.1365 220558 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.5 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12750 0 26 1339 14115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006213414
X-RAY DIFFRACTIONf_angle_d0.888418257
X-RAY DIFFRACTIONf_chiral_restr0.06051863
X-RAY DIFFRACTIONf_plane_restr0.00762465
X-RAY DIFFRACTIONf_dihedral_angle_d14.34554820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.33622930.30447050X-RAY DIFFRACTION99.74
1.62-1.640.30672950.27647068X-RAY DIFFRACTION99.97
1.64-1.660.30222910.25086983X-RAY DIFFRACTION99.95
1.66-1.680.26792940.22697056X-RAY DIFFRACTION99.93
1.68-1.70.25662920.20217003X-RAY DIFFRACTION99.88
1.7-1.720.26022950.19717085X-RAY DIFFRACTION99.96
1.72-1.750.2242920.16586993X-RAY DIFFRACTION99.89
1.75-1.770.20662920.15317027X-RAY DIFFRACTION99.92
1.77-1.80.20822940.14767055X-RAY DIFFRACTION99.86
1.8-1.830.19372950.13967070X-RAY DIFFRACTION99.92
1.83-1.860.20332920.14836999X-RAY DIFFRACTION99.92
1.86-1.90.19672920.1597024X-RAY DIFFRACTION99.88
1.9-1.930.20222940.16127060X-RAY DIFFRACTION99.97
1.93-1.970.19572950.13697074X-RAY DIFFRACTION99.95
1.97-2.020.17772920.12247000X-RAY DIFFRACTION99.95
2.02-2.060.17782940.12087054X-RAY DIFFRACTION99.97
2.06-2.110.16412960.12287098X-RAY DIFFRACTION99.92
2.11-2.170.16522910.1196995X-RAY DIFFRACTION99.9
2.17-2.240.16142940.1187053X-RAY DIFFRACTION99.92
2.24-2.310.16562950.12217075X-RAY DIFFRACTION99.89
2.31-2.390.15662930.1197046X-RAY DIFFRACTION99.96
2.39-2.490.15262960.12267092X-RAY DIFFRACTION99.95
2.49-2.60.16892930.12777037X-RAY DIFFRACTION99.86
2.6-2.740.1762940.13757057X-RAY DIFFRACTION99.93
2.74-2.910.17222950.14287079X-RAY DIFFRACTION99.93
2.91-3.130.16522950.14697082X-RAY DIFFRACTION99.69
3.13-3.450.14422940.13847059X-RAY DIFFRACTION99.69
3.45-3.950.14172980.12597142X-RAY DIFFRACTION99.96
3.95-4.970.11172950.10077099X-RAY DIFFRACTION99.8
4.97-47.10.12923020.12587220X-RAY DIFFRACTION99.52

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