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- PDB-5o4q: Crystal Structure of mutant M54L/M64L/M96L of Two-Domain Laccase ... -

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Basic information

Entry
Database: PDB / ID: 5o4q
TitleCrystal Structure of mutant M54L/M64L/M96L of Two-Domain Laccase from Streptomyces griseoflavus with 0.25 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
AZIDE ION / COPPER (II) ION / FORMIC ACID / Two-domain laccase
Similarity search - Component
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGabdulkhakov, A.G. / Tishchenko, T.V.
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 30, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)418,54245
Polymers416,37012
Non-polymers2,17233
Water13,529751
1
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,73012
Polymers104,0933
Non-polymers6389
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11640 Å2
ΔGint-81 kcal/mol
Surface area27620 Å2
MethodPISA
2
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,56211
Polymers104,0933
Non-polymers4698
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11380 Å2
ΔGint-77 kcal/mol
Surface area27460 Å2
MethodPISA
3
G: Two-domain laccase
H: Two-domain laccase
I: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,51610
Polymers104,0933
Non-polymers4237
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10920 Å2
ΔGint-79 kcal/mol
Surface area27410 Å2
MethodPISA
4
J: Two-domain laccase
K: Two-domain laccase
L: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,73412
Polymers104,0933
Non-polymers6429
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-88 kcal/mol
Surface area27630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.841, 94.850, 116.614
Angle α, β, γ (deg.)90.04, 90.29, 91.49
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) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4FJ81, laccase

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Non-polymers , 7 types, 784 molecules

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


Mass: 63.546 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 39.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / 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: 0.9793 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: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 235821 / % possible obs: 95.69 % / Redundancy: 3.4 % / Net I/σ(I): 6.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O3K

5o3k


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.541 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R Free: 0.14
RfactorNum. reflection% reflectionSelection details
Rfree0.21309 12501 5 %RANDOM
Rwork0.18718 ---
obs0.18846 235821 95.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.373 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å2-0.61 Å2-0.08 Å2
2---0.2 Å20.09 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25526 0 66 751 26343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01926362
X-RAY DIFFRACTIONr_bond_other_d0.0020.0223888
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.92135828
X-RAY DIFFRACTIONr_angle_other_deg1.96354921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32353336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19723.141261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.342153853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.91515180
X-RAY DIFFRACTIONr_chiral_restr0.0590.23707
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02130619
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026455
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9222.99513346
X-RAY DIFFRACTIONr_mcbond_other2.9232.99513345
X-RAY DIFFRACTIONr_mcangle_it3.9914.49516674
X-RAY DIFFRACTIONr_mcangle_other3.9914.49616675
X-RAY DIFFRACTIONr_scbond_it2.83.07113016
X-RAY DIFFRACTIONr_scbond_other2.7993.07113016
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7224.54619153
X-RAY DIFFRACTIONr_long_range_B_refined4.9823.65529207
X-RAY DIFFRACTIONr_long_range_B_other4.9823.65629208
X-RAY DIFFRACTIONr_rigid_bond_restr15.469350250
X-RAY DIFFRACTIONr_sphericity_free28.6875138
X-RAY DIFFRACTIONr_sphericity_bonded13.72550145
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 982 -
Rwork0.289 17061 -
obs--94.28 %

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