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- PDB-6rhq: Crystal Structure of Two-Domain Laccase mutant I170A from Strepto... -

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Basic information

Entry
Database: PDB / ID: 6rhq
TitleCrystal Structure of Two-Domain Laccase mutant I170A 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 / 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 / Two-domain laccase
Similarity search - Component
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsGabdulkhakov, A.G. / Tishchenko, T.V. / Kolyadenko, I.A.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-04-00270a 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
DepositionApr 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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

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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)210,15934
Polymers208,2576
Non-polymers1,90128
Water10,611589
1
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,89115
Polymers104,1293
Non-polymers76312
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)105,26819
Polymers104,1293
Non-polymers1,13916
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.790, 94.690, 116.490
Angle α, β, γ (deg.)90.00, 90.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Two-domain laccase


Mass: 34709.559 Da / Num. of mol.: 6
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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 1.98 Å3/Da / Density % sol: 37.89 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 25% Smear medium PEG, 0.1 M Bicine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.00318 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00318 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 112783 / % possible obs: 99.8 % / Redundancy: 6.72 % / Rrim(I) all: 0.135 / Net I/σ(I): 10.13
Reflection shellResolution: 1.98→2.03 Å / Num. unique obs: 8272 / CC1/2: 0.73 / Rrim(I) all: 0.952

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O4Q

5o4q


Resolution: 1.98→49.607 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 22.87
RfactorNum. reflection% reflection
Rfree0.2148 5674 5.03 %
Rwork0.174 --
obs0.1761 112768 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→49.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12793 0 46 589 13428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713229
X-RAY DIFFRACTIONf_angle_d0.85417976
X-RAY DIFFRACTIONf_dihedral_angle_d8.6539439
X-RAY DIFFRACTIONf_chiral_restr0.0621833
X-RAY DIFFRACTIONf_plane_restr0.0052407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.00250.29571730.24363514X-RAY DIFFRACTION100
2.0025-2.02610.30671870.24433571X-RAY DIFFRACTION100
2.0261-2.05080.27241810.2293567X-RAY DIFFRACTION100
2.0508-2.07670.2842190.22393543X-RAY DIFFRACTION100
2.0767-2.10410.28071680.21393544X-RAY DIFFRACTION100
2.1041-2.13290.26321930.20733577X-RAY DIFFRACTION100
2.1329-2.16340.26192120.20513510X-RAY DIFFRACTION100
2.1634-2.19570.26971850.20363620X-RAY DIFFRACTION100
2.1957-2.230.28211830.23503X-RAY DIFFRACTION100
2.23-2.26650.25071930.19733589X-RAY DIFFRACTION100
2.2665-2.30560.25062040.18783534X-RAY DIFFRACTION100
2.3056-2.34750.24931910.18863548X-RAY DIFFRACTION100
2.3475-2.39270.24231850.18173581X-RAY DIFFRACTION100
2.3927-2.44150.23861530.19263596X-RAY DIFFRACTION100
2.4415-2.49460.24291840.19473598X-RAY DIFFRACTION100
2.4946-2.55260.25682230.18523496X-RAY DIFFRACTION100
2.5526-2.61650.21352020.18123560X-RAY DIFFRACTION100
2.6165-2.68720.23691780.18453589X-RAY DIFFRACTION100
2.6872-2.76630.25572110.19263561X-RAY DIFFRACTION100
2.7663-2.85550.25871950.18573554X-RAY DIFFRACTION100
2.8555-2.95760.21471560.18523585X-RAY DIFFRACTION100
2.9576-3.0760.22881680.17873584X-RAY DIFFRACTION100
3.076-3.2160.21271750.18453568X-RAY DIFFRACTION100
3.216-3.38550.21252140.17933577X-RAY DIFFRACTION100
3.3855-3.59750.20281950.16713553X-RAY DIFFRACTION100
3.5975-3.87520.18411850.15863590X-RAY DIFFRACTION100
3.8752-4.2650.17071860.13913599X-RAY DIFFRACTION100
4.265-4.88170.14741810.12633595X-RAY DIFFRACTION100
4.8817-6.14860.16681800.14373623X-RAY DIFFRACTION100
6.1486-49.62230.20162140.17443665X-RAY DIFFRACTION100

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