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- PDB-6q29: Crystal structure of Laccase from Thermus thermophilus HB27 with ... -

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Basic information

Entry
Database: PDB / ID: 6q29
TitleCrystal structure of Laccase from Thermus thermophilus HB27 with an open conformation of beta-hairpin (Average deposted dose 2.5 MGy)
ComponentsLaccase
KeywordsSTRUCTURAL PROTEIN / open loop / 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
COPPER (II) ION / TRIETHYLENE GLYCOL / Laccase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.702 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 7, 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

Downloads & links

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Assembly

Deposited unit
A: Laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2635
Polymers48,7911
Non-polymers4714
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Proteins were loaded in superdex 75 column and eluted with 120 mL 20 mM MES and 50 mM NaCl.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.550, 62.760, 67.120
Angle α, β, γ (deg.)90.000, 93.880, 90.000
Int Tables number4
Space group name H-MP1211

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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) / Strain (production host): BL21(DE3) / References: UniProt: Q72HW2, laccase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.05 Å3/Da / Density % sol: 40.12 % / Description: triangular shaped sheets
Crystal growTemperature: 277.15 K / Method: batch mode / pH: 5.5
Details: 20% PEG 4000, 20% 2-propanol, 100 mM Citrate buffer
PH range: 5.5-5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0212 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2018 / Details: Sagittal focusing 2nd crystal horizontal focusing
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0212 Å / Relative weight: 1
ReflectionResolution: 1.7→33.15 Å / Num. obs: 45669 / % possible obs: 99.2 % / Redundancy: 3.68 % / Biso Wilson estimate: 11.9 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.42 / Net I/σ(I): 24.44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.83.628.773410.9820.1698.44
1.8-1.933.7212.5768650.9920.1199.2
1.93-2.083.7118.18239120.9950.07699.3
2.08-2.283.6923.91219580.9970.05699.4
2.28-2.553.6928.26199100.980.04699.3
2.55-2.943.6932.97175600.9980.03899.6
2.94-3.593.6940.15149530.9990.0399.5
3.59-5.063.647.76116230.9990.02699.3
5.06-33.143.647.8763800.9990.02598.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSVERSION Jan 26, 2018data reduction
XSCALEVERSION Jan 26, 2018data scaling
PHASER7.0.076phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XU9

5xu9


Resolution: 1.702→33.149 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 2174 4.76 %Random selection
Rwork0.1797 43492 --
obs0.1816 45666 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.23 Å2 / Biso mean: 16.8935 Å2 / Biso min: 1.77 Å2
Refinement stepCycle: final / Resolution: 1.702→33.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 25 417 3881
Biso mean--27.17 24.75 -
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 (%)
1.7021-1.73910.26651190.2037269498
1.7391-1.77960.26481470.2091267499
1.7796-1.82410.25141300.2067269699
1.8241-1.87340.24251100.1997275499
1.8734-1.92850.22961240.1978269199
1.9285-1.99080.25911190.1882270399
1.9908-2.06190.23631290.18892736100
2.0619-2.14450.23461470.18932693100
2.1445-2.2420.2261180.1911276599
2.242-2.36020.24121420.1907267099
2.3602-2.5080.21521610.19042731100
2.508-2.70160.25531320.19612748100
2.7016-2.97330.23951640.19262707100
2.9733-3.40320.18781600.1736269799
3.4032-4.28620.18411350.1452274499
4.2862-33.140.1871370.1475278999

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