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- PDB-6w9x: Crystal structure of Laccase from Thermus thermophilus HB27 with ... -

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Basic information

Entry
Database: PDB / ID: 6w9x
TitleCrystal structure of Laccase from Thermus thermophilus HB27 with an open conformation of beta-hairpin (Average deposited dose 5.1 MGy)
ComponentsLaccase
KeywordsOXIDOREDUCTASE / open conformation / 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, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / Laccase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMiranda-Blancas, R. / Rudino-Pinera, E.
CitationJournal: To Be Published
Title: Dynamic behavior of alpha-hairpin loop at laccase of Thermus thermophilus at 1.7 angstroms resolution.
Authors: Miranda-Blancas, R. / Rudino-Pinera, E.
History
DepositionMar 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)49,2144
Polymers48,8491
Non-polymers3653
Water8,017445
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)54.521, 60.757, 76.338
Angle α, β, γ (deg.)90.000, 109.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Laccase


Mass: 48848.512 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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.44 Å3/Da / Density % sol: 49.58 % / Description: triangular shaped sheets
Crystal growTemperature: 277.15 K / Method: batch mode / pH: 5.5 / Details: 20% PEG 4000, 20% 2-propanol, 100mM 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: 1.195 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2018 / Details: Sagittal focusing 2nd crystal horizontal focusing
RadiationMonochromator: Si (111) Rosenbaum-Rock / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.195 Å / Relative weight: 1
ReflectionResolution: 1.7→39.24 Å / Num. obs: 51847 / % possible obs: 99.98 % / Redundancy: 8.7 % / Biso Wilson estimate: 16.2 Å2 / CC1/2: 0.75 / CC star: 0.928 / Rmerge(I) obs: 0.7079 / Rpim(I) all: 0.2518 / Rrim(I) all: 0.752 / Net I/σ(I): 55.41
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.266 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 5145 / CC1/2: 0.539 / Rpim(I) all: 0.461 / Rrim(I) all: 1.35 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSVersion Jan 26,201data reduction
XSCALEVersion Jan 26,201data scaling
PHASER7.0.076phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XU9

2xu9


Resolution: 1.7→39.24 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2468 2610 5.03 %
Rwork0.1979 49237 -
obs0.2004 51847 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.55 Å2 / Biso mean: 21.2788 Å2 / Biso min: 4.04 Å2
Refinement stepCycle: final / Resolution: 1.7→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3443 0 17 445 3905
Biso mean--26.67 29.93 -
Num. residues----440
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.730.32691390.301725672706
1.73-1.760.30721420.28325612703
1.76-1.80.31621330.262625692702
1.8-1.840.281380.245625732711
1.84-1.880.29971340.236125802714
1.88-1.930.28721420.238125672709
1.93-1.980.3161360.219125862722
1.98-2.040.27931230.221926062729
2.04-2.110.23221540.216925692723
2.11-2.180.27721180.200426052723
2.18-2.270.26751410.198225842725
2.27-2.370.26771440.189325662710
2.37-2.50.261470.193725842731
2.5-2.650.23541200.190926132733
2.65-2.860.24771250.198826062731
2.86-3.140.2431750.197725712746
3.14-3.60.23131240.183226242748
3.6-4.530.20861200.159926422762
4.53-39.240.18991550.170326642819

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