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- PDB-5mkm: Crystal Structure of Two-Domain Laccase mutant H165F from Strepto... -

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Basic information

Entry
Database: PDB / ID: 5mkm
TitleCrystal Structure of Two-Domain Laccase mutant H165F from Streptomyces griseoflavus
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: 1.996 Å
AuthorsGabdulkhakov, A.G. / Tishchenko, T.V.
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 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: 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 / 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.pdbx_ptnr1_label_alt_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,73526
Polymers208,5646
Non-polymers1,17120
Water5,116284
1
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,77312
Polymers104,2823
Non-polymers4919
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-80 kcal/mol
Surface area27450 Å2
MethodPISA
2
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,96114
Polymers104,2823
Non-polymers67911
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11710 Å2
ΔGint-83 kcal/mol
Surface area27260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.884, 95.075, 116.821
Angle α, β, γ (deg.)90.00, 90.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Two-domain laccase


Mass: 34760.664 Da / Num. of mol.: 6
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 , 7 types, 304 molecules

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


Mass: 63.546 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: 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
#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.: 284 / 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: 39.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 20% PEG 6000, 0.1 M Bicine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.980583 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980583 Å / Relative weight: 1
ReflectionResolution: 1.996→50 Å / Num. obs: 206927 / % possible obs: 80.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.29 % / CC1/2: 0.99 / Net I/σ(I): 5.41
Reflection shellResolution: 1.996→2.12 Å / Redundancy: 2.06 % / Mean I/σ(I) obs: 1.49 / CC1/2: 0.69 / % possible all: 78.9

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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: 1.996→49.767 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 26.46
RfactorNum. reflection% reflection
Rfree0.2332 3565 1.99 %
Rwork0.1997 --
obs0.2004 178976 80.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.996→49.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12736 0 37 284 13057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813206
X-RAY DIFFRACTIONf_angle_d0.92817937
X-RAY DIFFRACTIONf_dihedral_angle_d19.9744706
X-RAY DIFFRACTIONf_chiral_restr0.061832
X-RAY DIFFRACTIONf_plane_restr0.0062395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9964-2.02370.35911170.31945785X-RAY DIFFRACTION66
2.0237-2.05260.32771550.30496859X-RAY DIFFRACTION79
2.0526-2.08330.37521150.29157462X-RAY DIFFRACTION86
2.0833-2.11580.32971410.28627417X-RAY DIFFRACTION85
2.1158-2.15050.3421990.27967348X-RAY DIFFRACTION85
2.1505-2.18760.30991360.27747414X-RAY DIFFRACTION85
2.1876-2.22740.32641730.27617272X-RAY DIFFRACTION84
2.2274-2.27020.36081490.25797300X-RAY DIFFRACTION84
2.2702-2.31650.29411160.24947300X-RAY DIFFRACTION83
2.3165-2.36690.27041000.22787081X-RAY DIFFRACTION81
2.3669-2.4220.25111140.22077117X-RAY DIFFRACTION82
2.422-2.48250.26251440.22117306X-RAY DIFFRACTION84
2.4825-2.54970.2571660.22077206X-RAY DIFFRACTION83
2.5497-2.62470.27791370.22027189X-RAY DIFFRACTION82
2.6247-2.70940.26771370.21847229X-RAY DIFFRACTION82
2.7094-2.80620.25791760.21266982X-RAY DIFFRACTION81
2.8062-2.91860.24231610.19886773X-RAY DIFFRACTION78
2.9186-3.05140.25591290.19787058X-RAY DIFFRACTION81
3.0514-3.21220.22331200.1957053X-RAY DIFFRACTION81
3.2122-3.41340.17761360.1826977X-RAY DIFFRACTION80
3.4134-3.67690.1911730.16866778X-RAY DIFFRACTION78
3.6769-4.04680.21781500.1626666X-RAY DIFFRACTION77
4.0468-4.6320.15371350.146804X-RAY DIFFRACTION79
4.632-5.83440.17551620.14926541X-RAY DIFFRACTION75
5.8344-49.78210.18741240.17126494X-RAY DIFFRACTION75

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