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- PDB-6fc7: Crystal Structure of Two-Domain Laccase mutant H165F from Strepto... -

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Basic information

Entry
Database: PDB / ID: 6fc7
TitleCrystal Structure of Two-Domain Laccase mutant H165F 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 / 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 / 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 / PEROXIDE ION / Two-domain laccase
Similarity search - Component
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 20, 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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)420,52669
Polymers417,12812
Non-polymers3,39857
Water10,485582
1
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,16917
Polymers104,2823
Non-polymers88714
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12340 Å2
ΔGint-155 kcal/mol
Surface area27220 Å2
MethodPISA
2
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,14118
Polymers104,2823
Non-polymers85915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11860 Å2
ΔGint-154 kcal/mol
Surface area27140 Å2
MethodPISA
3
G: Two-domain laccase
H: Two-domain laccase
I: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,07716
Polymers104,2823
Non-polymers79513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11950 Å2
ΔGint-152 kcal/mol
Surface area27350 Å2
MethodPISA
4
J: Two-domain laccase
K: Two-domain laccase
L: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,14118
Polymers104,2823
Non-polymers85915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12350 Å2
ΔGint-151 kcal/mol
Surface area26990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.025, 94.585, 115.931
Angle α, β, γ (deg.)90.00, 90.00, 92.01
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Two-domain laccase


Mass: 34760.664 Da / Num. of mol.: 12
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

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Non-polymers , 5 types, 639 molecules

#2: Chemical...
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-PER / PEROXIDE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 2.02 Å3/Da / Density % sol: 39.22 %
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: 1.27516 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27516 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 235591 / % possible obs: 94.3 % / Redundancy: 3.59 % / Net I/σ(I): 7.88
Reflection shellResolution: 1.92→2.05 Å / Mean I/σ(I) obs: 1.57 / Num. unique obs: 41396 / % possible all: 92.9

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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: 5MKM

5mkm


Resolution: 1.95→49.415 Å / Cross valid method: FREE R-VALUE / σ(F): 7.6 / Phase error: 33.13
RfactorNum. reflection% reflection
Rfree0.231 11297 5.38 %
Rwork0.1947 --
obs0.2121 225948 92.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→49.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25720 0 70 582 26372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826577
X-RAY DIFFRACTIONf_angle_d0.99536101
X-RAY DIFFRACTIONf_dihedral_angle_d8.28619482
X-RAY DIFFRACTIONf_chiral_restr0.0593687
X-RAY DIFFRACTIONf_plane_restr0.0074834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.98370.328111540.308620608X-RAY DIFFRACTION86
1.9837-2.01970.335911040.308720791X-RAY DIFFRACTION87
2.0197-2.05860.333410160.301520202X-RAY DIFFRACTION85
2.0586-2.10060.318411430.294120892X-RAY DIFFRACTION87
2.1006-2.14620.31939030.29121173X-RAY DIFFRACTION88
2.1462-2.19610.309911630.291220753X-RAY DIFFRACTION87
2.1961-2.2510.3311300.290820799X-RAY DIFFRACTION88
2.251-2.31190.320511070.281620890X-RAY DIFFRACTION88
2.3119-2.37980.311211200.272820737X-RAY DIFFRACTION87
2.3798-2.45660.314111200.268520472X-RAY DIFFRACTION86
2.4566-2.54440.305711440.266321156X-RAY DIFFRACTION89
2.5444-2.64620.296911030.251821194X-RAY DIFFRACTION89
2.6462-2.76650.290210530.247521252X-RAY DIFFRACTION89
2.7665-2.91220.270110280.232321246X-RAY DIFFRACTION89
2.9122-3.09450.26029490.219721262X-RAY DIFFRACTION89
3.0945-3.3330.255610510.208121402X-RAY DIFFRACTION90
3.333-3.66780.232411030.182321420X-RAY DIFFRACTION90
3.6678-4.1970.210413190.163421123X-RAY DIFFRACTION89
4.197-5.28210.173412300.136521105X-RAY DIFFRACTION88
5.2821-28.09960.186611770.159321557X-RAY DIFFRACTION90

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