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- PDB-6fdj: Crystal Structure of Two-Domain Laccase mutant H165A from Strepto... -

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Basic information

Entry
Database: PDB / ID: 6fdj
TitleCrystal Structure of Two-Domain Laccase mutant H165A from Streptomyces griseoflavus with high copper ions occupancy
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 / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence ...Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / OXYGEN MOLECULE / Two-domain laccase
Similarity search - Component
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.308 Å
AuthorsGabdulkhakov, A.G. / Tishchenko, T.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research Russian Federation
CitationJournal: Int J Mol Sci / Year: 2019
Title: Investigations of Accessibility of T2/T3 Copper Center of Two-Domain Laccase fromStreptomyces griseoflavusAc-993.
Authors: Gabdulkhakov, A. / Kolyadenko, I. / Kostareva, O. / Mikhaylina, A. / Oliveira, P. / Tamagnini, P. / Lisov, A. / Tishchenko, S.
History
DepositionDec 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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)420,56278
Polymers416,21512
Non-polymers4,34766
Water5,459303
1
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,97218
Polymers104,0543
Non-polymers91915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11790 Å2
ΔGint-142 kcal/mol
Surface area27340 Å2
MethodPISA
2
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,21720
Polymers104,0543
Non-polymers1,16317
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12660 Å2
ΔGint-150 kcal/mol
Surface area26950 Å2
MethodPISA
3
G: Two-domain laccase
H: Two-domain laccase
I: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,12519
Polymers104,0543
Non-polymers1,07116
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12250 Å2
ΔGint-148 kcal/mol
Surface area27120 Å2
MethodPISA
4
J: Two-domain laccase
K: Two-domain laccase
L: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,24921
Polymers104,0543
Non-polymers1,19518
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12620 Å2
ΔGint-144 kcal/mol
Surface area26980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.369, 95.118, 116.475
Angle α, β, γ (deg.)90.13, 90.11, 91.85
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Two-domain laccase


Mass: 34684.570 Da / Num. of mol.: 12 / Mutation: H165A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseoflavus (bacteria) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4FJ81, laccase
#2: Chemical...
ChemComp-CU / COPPER (II) ION


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


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 6K, 0.1M Bicine, pH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.033121 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033121 Å / Relative weight: 1
ReflectionResolution: 2.308→50 Å / Num. obs: 143173 / % possible obs: 98 % / Redundancy: 3.54 % / Net I/σ(I): 9.35
Reflection shellResolution: 2.31→2.45 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LHL

5lhl


Resolution: 2.308→49.712 Å / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 32.53
RfactorNum. reflection% reflection
Rfree0.2221 7282 5.09 %
Rwork0.1709 --
obs0.1826 143173 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.308→49.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25402 0 132 303 25837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826200
X-RAY DIFFRACTIONf_angle_d0.96135558
X-RAY DIFFRACTIONf_dihedral_angle_d8.45415441
X-RAY DIFFRACTIONf_chiral_restr0.0573647
X-RAY DIFFRACTIONf_plane_restr0.0064740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3093-2.34910.30832890.26666693X-RAY DIFFRACTION92
2.3491-2.39180.27263820.24976726X-RAY DIFFRACTION92
2.3918-2.43770.33650.25686760X-RAY DIFFRACTION93
2.4377-2.48750.3323520.25416772X-RAY DIFFRACTION93
2.4875-2.54150.3343230.24776809X-RAY DIFFRACTION93
2.5415-2.60060.30983640.24496730X-RAY DIFFRACTION93
2.6006-2.66560.33610.24416825X-RAY DIFFRACTION93
2.6656-2.73770.31934040.2356726X-RAY DIFFRACTION93
2.7377-2.81810.29144160.22976694X-RAY DIFFRACTION92
2.8181-2.9090.29553360.21416835X-RAY DIFFRACTION94
2.909-3.01290.27283490.21016821X-RAY DIFFRACTION94
3.0129-3.13340.27213880.19896755X-RAY DIFFRACTION93
3.1334-3.27590.25453550.19126868X-RAY DIFFRACTION94
3.2759-3.44830.24663200.17396821X-RAY DIFFRACTION94
3.4483-3.6640.22583630.16396894X-RAY DIFFRACTION94
3.664-3.94630.20443270.15616792X-RAY DIFFRACTION94
3.9463-4.34230.1864020.13876815X-RAY DIFFRACTION93
4.3423-4.96810.15723620.12156876X-RAY DIFFRACTION94
4.9681-6.24970.16083230.13446869X-RAY DIFFRACTION95
6.2497-29.66340.18453790.1616837X-RAY DIFFRACTION94

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