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- PDB-7puh: Crystal Structure of Two-Domain Laccase mutant H165A/R240H from S... -

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Basic information

Entry
Database: PDB / ID: 7puh
TitleCrystal Structure of Two-Domain Laccase mutant H165A/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 / DI(HYDROXYETHYL)ETHER / Two-domain laccase
Similarity search - Component
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKolyadenko, I. / Tishchenko, S. / Gabdulkhakov, A.
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 30, 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)183,85046
Polymers181,2166
Non-polymers2,63440
Water29,7071649
1
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,16725
Polymers90,6083
Non-polymers1,55922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,68321
Polymers90,6083
Non-polymers1,07518
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.760, 94.286, 120.482
Angle α, β, γ (deg.)90.000, 91.273, 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: 30202.594 Da / Num. of mol.: 6 / Mutation: H165A/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 , 7 types, 1689 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-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1649 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
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 condition #31 of BCS-1 from Molecular Dimensions, UK

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 405781 / % possible obs: 99.1 % / Redundancy: 6.76 % / Biso Wilson estimate: 15.89 Å2 / CC1/2: 1 / Net I/σ(I): 18.19
Reflection shellResolution: 1.3→1.38 Å / Redundancy: 6.35 % / Mean I/σ(I) obs: 1.28 / Num. unique obs: 64031 / CC1/2: 0.55 / % possible all: 97

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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: 1.3→47.41 Å / SU ML: 0.1419 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.7241
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1569 20408 5.03 %
Rwork0.1326 385285 -
obs0.1338 405693 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.75 Å2
Refinement stepCycle: LAST / Resolution: 1.3→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12734 0 96 1649 14479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005614746
X-RAY DIFFRACTIONf_angle_d0.867220152
X-RAY DIFFRACTIONf_chiral_restr0.08762041
X-RAY DIFFRACTIONf_plane_restr0.00592751
X-RAY DIFFRACTIONf_dihedral_angle_d13.96725419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.34016880.31212138X-RAY DIFFRACTION94.71
1.31-1.330.30016870.260612791X-RAY DIFFRACTION99.1
1.33-1.350.2866460.24512758X-RAY DIFFRACTION98.92
1.35-1.360.24866330.232612753X-RAY DIFFRACTION98.3
1.36-1.380.24776920.220812578X-RAY DIFFRACTION97.36
1.38-1.40.23876550.202512892X-RAY DIFFRACTION99.92
1.4-1.420.22127060.191112814X-RAY DIFFRACTION99.84
1.42-1.440.21536700.169912912X-RAY DIFFRACTION99.81
1.44-1.460.20217540.1612863X-RAY DIFFRACTION99.8
1.46-1.490.21077060.160112864X-RAY DIFFRACTION99.8
1.49-1.510.19296830.150512819X-RAY DIFFRACTION99.74
1.51-1.540.19356850.146312916X-RAY DIFFRACTION99.67
1.54-1.570.17987020.138812791X-RAY DIFFRACTION99.6
1.57-1.60.16586710.125712849X-RAY DIFFRACTION99.32
1.6-1.640.14516850.112712788X-RAY DIFFRACTION99.12
1.64-1.680.15536530.11612798X-RAY DIFFRACTION98.74
1.68-1.720.14936600.112812694X-RAY DIFFRACTION97.92
1.72-1.760.15086950.108112898X-RAY DIFFRACTION99.99
1.76-1.820.14067080.107412919X-RAY DIFFRACTION99.99
1.82-1.870.13736990.109312953X-RAY DIFFRACTION99.97
1.87-1.940.15087040.123112912X-RAY DIFFRACTION99.99
1.94-2.020.14467200.114712873X-RAY DIFFRACTION99.82
2.02-2.110.14526800.116912916X-RAY DIFFRACTION99.75
2.11-2.220.14996630.116812904X-RAY DIFFRACTION99.41
2.22-2.360.14776340.124612839X-RAY DIFFRACTION98.72
2.36-2.540.15496270.130312903X-RAY DIFFRACTION99
2.54-2.80.16947200.138112955X-RAY DIFFRACTION99.96
2.8-3.210.15887010.135812972X-RAY DIFFRACTION99.96
3.21-4.040.13256570.128413053X-RAY DIFFRACTION99.62
4.04-47.410.12936240.122313170X-RAY DIFFRACTION99.03

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