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- PDB-6tyr: Crystal structure of Laccase from Thermus thermophilus HB27 with ... -

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Basic information

Entry
Database: PDB / ID: 6tyr
TitleCrystal structure of Laccase from Thermus thermophilus HB27 with a close conformation of its beta-hairpin
ComponentsLaccase
KeywordsOXIDOREDUCTASE / close loop / laccase / multicopper oxidase
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, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin
Similarity search - Domain/homology
CITRIC ACID / COPPER (II) ION / Laccase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.813 Å
AuthorsMiranda-Blancas, R. / Rudino-Pinera, E.
CitationJournal: J.Struct.Biol. / Year: 2021
Title: The beta-hairpin from the Thermus thermophilus HB27 laccase works as a pH-dependent switch to regulate laccase activity.
Authors: Miranda-Blancas, R. / Avelar, M. / Rodriguez-Arteaga, A. / Sinicropi, A. / Rudino-Pinera, E.
History
DepositionAug 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4518
Polymers48,7911
Non-polymers6597
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein was loaded at superdex 75 column and eluted woth MES pH 5.5 20 mM and 50 mM NaCl
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.445, 85.386, 169.156
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-276-

ARG

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Components

#1: Protein Laccase / / multicopper oxidase


Mass: 48791.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1370 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72HW2, laccase
#2: 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
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 277.15 K / Method: microbatch / pH: 5.5
Details: 20% PEG 4000, 20% 2-propanol, 100 mM sodium citrate pH 5.5
PH range: 5.5-5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 25, 2018 / Details: OSMIC VARIMAX CU-HF
RadiationMonochromator: Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.81→42.29 Å / Num. obs: 39303 / % possible obs: 96.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 23.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0307 / Rpim(I) all: 0.0307 / Rrim(I) all: 0.043 / Net I/σ(I): 25.62
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.81-1.881.90.3472.934300.6820.3470.49185.4
1.88-1.951.90.2454.138130.820.2450.34695
1.95-2.041.90.1685.938450.8990.1680.23795.6
2.04-2.151.90.128.138620.9460.120.1796.5
2.15-2.281.90.0911.239430.9670.090.12796.9
2.28-2.461.90.06914.239410.9810.0690.09797.4
2.46-2.711.90.05418.839970.9870.0540.07798.7
2.71-3.120.0332.741010.9960.030.04399.8
3.1-3.9120.0255.841080.9980.020.02899.9
3.91-42.2920.01391.342630.9990.0130.01899.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACK7.0.076data scaling
PHASER7.0.076phasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XU9

2xu9


Resolution: 1.813→42.29 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.43
RfactorNum. reflection% reflection
Rfree0.2332 1908 4.86 %
Rwork0.1806 --
obs0.1831 39244 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.99 Å2 / Biso mean: 27.8254 Å2 / Biso min: 9.52 Å2
Refinement stepCycle: final / Resolution: 1.813→42.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 34 290 3763
Biso mean--41.24 36.28 -
Num. residues----439
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8134-1.85870.3279950.2824223282
1.8587-1.9090.31191230.2656256394
1.909-1.96510.33871560.2358258595
1.9651-2.02860.28691370.2123263396
2.0286-2.10110.26351270.2136263096
2.1011-2.18520.24261540.2024263397
2.1852-2.28460.26351230.1976268297
2.2846-2.40510.24961250.1883268697
2.4051-2.55580.26041380.1921268398
2.5558-2.75310.23781360.1856276599
2.7531-3.030.21271420.1784272899
3.03-3.46830.22191540.16532787100
3.4683-4.3690.19711540.14522806100
4.369-42.290.20951440.1662923100

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