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- PDB-7ptm: Crystal Structure of Two-Domain Laccase mutant M199G/R240H from S... -

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Basic information

Entry
Database: PDB / ID: 7ptm
TitleCrystal Structure of Two-Domain Laccase mutant M199G/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 / copper ion binding
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 / MOLECULAR REPLACEMENT / Resolution: 1.85 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
DepositionSep 27, 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)187,00436
Polymers185,2276
Non-polymers1,77730
Water14,412800
1
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,56419
Polymers92,6143
Non-polymers95116
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12250 Å2
ΔGint-152 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)93,44017
Polymers92,6143
Non-polymers82714
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11740 Å2
ΔGint-154 kcal/mol
Surface area27260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.064, 93.726, 119.233
Angle α, β, γ (deg.)90.000, 91.295, 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: 30871.211 Da / Num. of mol.: 6 / Mutation: M199G, 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
#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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-OXY / OXYGEN MOLECULE


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


Mass: 18.015 Da / Num. of mol.: 800 / 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: 2.24 Å3/Da / Density % sol: 45.04 %
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: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54178 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Sep 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.85→25 Å / Num. obs: 138143 / % possible obs: 99.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.3 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.164 / Rrim(I) all: 0.192 / Net I/σ(I): 6.96
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 1 / Num. unique obs: 6533 / CC1/2: 0.51 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PHENIX1.19.2_4158refinement
CrysalisPro40.84adata reduction
CrysalisPro40.84adata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LHL

5lhl


Resolution: 1.85→24.68 Å / SU ML: 0.2326 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.3082
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2235 6894 4.99 %
Rwork0.1832 131174 -
obs0.1851 138068 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.24 Å2
Refinement stepCycle: LAST / Resolution: 1.85→24.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12710 0 40 800 13550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007513263
X-RAY DIFFRACTIONf_angle_d0.968318043
X-RAY DIFFRACTIONf_chiral_restr0.0631845
X-RAY DIFFRACTIONf_plane_restr0.00772420
X-RAY DIFFRACTIONf_dihedral_angle_d14.74174704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.37022020.31764113X-RAY DIFFRACTION93.82
1.87-1.890.37782300.30674393X-RAY DIFFRACTION99.74
1.89-1.910.32362470.27334320X-RAY DIFFRACTION99.89
1.91-1.940.29782610.25254381X-RAY DIFFRACTION99.89
1.94-1.960.31362120.23524392X-RAY DIFFRACTION99.89
1.96-1.990.28212450.2244417X-RAY DIFFRACTION99.94
1.99-2.020.26712450.21984374X-RAY DIFFRACTION99.89
2.02-2.050.23982450.21084342X-RAY DIFFRACTION99.76
2.05-2.080.2412340.20734346X-RAY DIFFRACTION99.83
2.08-2.120.27142240.20484430X-RAY DIFFRACTION99.66
2.12-2.150.25592440.2094308X-RAY DIFFRACTION99.74
2.15-2.190.25111980.20014416X-RAY DIFFRACTION99.55
2.19-2.230.24681930.1934444X-RAY DIFFRACTION99.51
2.23-2.280.23232340.19454325X-RAY DIFFRACTION99.5
2.28-2.330.26412470.20094381X-RAY DIFFRACTION99.29
2.33-2.380.23972210.19154380X-RAY DIFFRACTION99.31
2.38-2.440.25082460.19274344X-RAY DIFFRACTION99.11
2.44-2.510.24272230.19164348X-RAY DIFFRACTION99.18
2.51-2.580.25132200.18554401X-RAY DIFFRACTION99.01
2.58-2.670.2262120.18644364X-RAY DIFFRACTION99.07
2.67-2.760.22472860.18514302X-RAY DIFFRACTION99.24
2.76-2.870.22712270.18464383X-RAY DIFFRACTION99.27
2.87-30.22092380.18954361X-RAY DIFFRACTION99.22
3-3.160.1922500.17984400X-RAY DIFFRACTION99.47
3.16-3.360.21632130.17314419X-RAY DIFFRACTION99.55
3.36-3.610.18831880.15924456X-RAY DIFFRACTION99.74
3.61-3.980.19592120.15654431X-RAY DIFFRACTION99.7
3.98-4.550.14342170.12514436X-RAY DIFFRACTION99.74
4.55-5.720.14582490.12614413X-RAY DIFFRACTION99.36
5.72-24.680.1742310.15044354X-RAY DIFFRACTION95.86

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