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- PDB-7pu0: Crystal Structure of Two-Domain Laccase mutant H165A/M199G from S... -

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Basic information

Entry
Database: PDB / ID: 7pu0
TitleCrystal Structure of Two-Domain Laccase mutant H165A/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 / Two-domain laccase
Similarity search - Component
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 28, 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)186,08432
Polymers184,5136
Non-polymers1,57126
Water9,782543
1
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,04216
Polymers92,2563
Non-polymers78613
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11580 Å2
ΔGint-151 kcal/mol
Surface area27730 Å2
MethodPISA
2
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,04216
Polymers92,2563
Non-polymers78613
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11450 Å2
ΔGint-154 kcal/mol
Surface area27660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.235, 94.591, 120.867
Angle α, β, γ (deg.)90.000, 91.388, 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: 30752.107 Da / Num. of mol.: 6 / Mutation: H165A/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.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
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: Dec 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 85543 / % possible obs: 98.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 22.89 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.19 / Net I/σ(I): 6.1
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4591 / CC1/2: 0.52 / % possible all: 98.7

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Processing

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

5lhl


Resolution: 2.2→24.74 Å / SU ML: 0.1996 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.9568
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1885 3328 3.89 %
Rwork0.1573 82130 -
obs0.1585 85458 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.96 Å2
Refinement stepCycle: LAST / Resolution: 2.2→24.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12704 0 26 543 13273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006913128
X-RAY DIFFRACTIONf_angle_d0.8917846
X-RAY DIFFRACTIONf_chiral_restr0.05671827
X-RAY DIFFRACTIONf_plane_restr0.00752395
X-RAY DIFFRACTIONf_dihedral_angle_d23.45764666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.25931110.23873430X-RAY DIFFRACTION98.22
2.23-2.260.27461260.22483479X-RAY DIFFRACTION99.97
2.26-2.30.22791360.22123506X-RAY DIFFRACTION99.89
2.3-2.340.25341460.21983450X-RAY DIFFRACTION99.97
2.34-2.380.24871570.21763445X-RAY DIFFRACTION99.86
2.38-2.420.27311350.21353466X-RAY DIFFRACTION99.81
2.42-2.470.2311190.21473511X-RAY DIFFRACTION99.81
2.47-2.520.22411430.2093431X-RAY DIFFRACTION99.64
2.52-2.570.23411870.20933426X-RAY DIFFRACTION99.64
2.57-2.630.24191470.20073467X-RAY DIFFRACTION99.45
2.63-2.70.22341480.19383459X-RAY DIFFRACTION99.42
2.7-2.770.2351470.19253410X-RAY DIFFRACTION99.22
2.77-2.850.19421330.18243446X-RAY DIFFRACTION99.14
2.85-2.940.23011480.1763477X-RAY DIFFRACTION98.99
2.94-3.050.20531340.17043448X-RAY DIFFRACTION98.76
3.05-3.170.20991400.163404X-RAY DIFFRACTION98.64
3.17-3.320.1531340.1583452X-RAY DIFFRACTION98.41
3.32-3.490.16711170.13573451X-RAY DIFFRACTION98.13
3.49-3.710.17941600.12513384X-RAY DIFFRACTION97.63
3.71-3.990.15151580.12153360X-RAY DIFFRACTION97.16
3.99-4.390.13991330.10153386X-RAY DIFFRACTION96.15
4.39-5.020.1121380.10033337X-RAY DIFFRACTION95.05
5.02-6.310.14851040.11173305X-RAY DIFFRACTION92.71
6.31-24.740.13861270.12993200X-RAY DIFFRACTION88.91

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