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- PDB-5o3k: Crystal Structure of mutant M54L/M64L/M96L of Two-Domain Laccase ... -

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Basic information

Entry
Database: PDB / ID: 5o3k
TitleCrystal Structure of mutant M54L/M64L/M96L of Two-Domain Laccase from Streptomyces griseoflavus with 1 mM copper sulfate on growth medium
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 / Multicopper oxidase, C-terminal / 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 / Multicopper oxidase, C-terminal / 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 ATOM / OXYGEN MOLECULE / Two-domain laccase
Similarity search - Component
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGabdulkhakov, A.G. / Tishchenko, T.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
RFBR15-04-03002 Russian Federation
CitationJournal: Mol.Biol.(Moscow) / Year: 2018
Title: Incorporation of Copper Ions into T2/T3 Centers of Two-Domain Laccases.
Authors: Gabdulkhakov, A.G. / Kostareva, O.S. / Kolyadenko, I.A. / Mikhaylina, A.O. / Trubitsina, L.I. / Tishchenko, S.V.
History
DepositionMay 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 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)419,23657
Polymers416,37012
Non-polymers2,86645
Water2,468137
1
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,86515
Polymers104,0933
Non-polymers77212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11840 Å2
ΔGint-111 kcal/mol
Surface area27430 Å2
MethodPISA
2
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,76014
Polymers104,0933
Non-polymers66711
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11370 Å2
ΔGint-121 kcal/mol
Surface area27780 Å2
MethodPISA
3
G: Two-domain laccase
H: Two-domain laccase
I: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,79214
Polymers104,0933
Non-polymers69911
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11460 Å2
ΔGint-138 kcal/mol
Surface area27820 Å2
MethodPISA
4
J: Two-domain laccase
K: Two-domain laccase
L: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,82014
Polymers104,0933
Non-polymers72811
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11690 Å2
ΔGint-126 kcal/mol
Surface area27490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.027, 94.957, 116.456
Angle α, β, γ (deg.)89.88, 90.07, 91.70
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: 34697.523 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: mutations M54L, M64L, M96L / 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, 182 molecules

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


Mass: 63.546 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 23% PEG 4000, 0,05M TRIS-HCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 176795 / % possible obs: 91.8 % / Redundancy: 2.06 % / Net I/σ(I): 4.57

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Processing

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

5lhl


Resolution: 2.1→49.585 Å / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 27.01
RfactorNum. reflection% reflection
Rfree0.2617 19018 5.38 %
Rwork0.1962 --
obs0.2046 176610 91.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→49.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25623 0 61 137 25821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00926461
X-RAY DIFFRACTIONf_angle_d1.05435987
X-RAY DIFFRACTIONf_dihedral_angle_d21.4379378
X-RAY DIFFRACTIONf_chiral_restr0.0623711
X-RAY DIFFRACTIONf_plane_restr0.0074810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1019-2.13810.32229320.288116588X-RAY DIFFRACTION86
2.1381-2.1770.33099340.283216601X-RAY DIFFRACTION86
2.177-2.21890.32348280.279116701X-RAY DIFFRACTION87
2.2189-2.26420.32378220.267216200X-RAY DIFFRACTION84
2.2642-2.31340.34377800.26816540X-RAY DIFFRACTION86
2.3134-2.36720.33658660.263216887X-RAY DIFFRACTION88
2.3672-2.42640.34339400.264216799X-RAY DIFFRACTION87
2.4264-2.4920.32797340.264116926X-RAY DIFFRACTION88
2.492-2.56530.31229420.258216620X-RAY DIFFRACTION87
2.5653-2.64810.32938340.246416527X-RAY DIFFRACTION86
2.6481-2.74270.28679040.236116272X-RAY DIFFRACTION85
2.7427-2.85250.32329240.225516409X-RAY DIFFRACTION85
2.8525-2.98230.30318540.209916936X-RAY DIFFRACTION89
2.9823-3.13940.26548720.196216934X-RAY DIFFRACTION88
3.1394-3.3360.27749360.188317226X-RAY DIFFRACTION89
3.336-3.59340.24828500.178216764X-RAY DIFFRACTION88
3.5934-3.95470.234211160.16617008X-RAY DIFFRACTION88
3.9547-4.52620.20469620.138717128X-RAY DIFFRACTION89
4.5262-5.69960.17269380.128616840X-RAY DIFFRACTION88
5.6996-38.66350.22758900.174217340X-RAY DIFFRACTION90

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