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- PDB-5jx9: Crystal structure of laccase from Thermus thermophilus HB27 (Cu(I... -

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Basic information

Entry
Database: PDB / ID: 5jx9
TitleCrystal structure of laccase from Thermus thermophilus HB27 (Cu(II)-cyclophanes, 5 min)
ComponentsLaccase
KeywordsOXIDOREDUCTASE / multicopper oxidases
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 / Cupredoxins - blue copper proteins ...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 / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Laccase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å
AuthorsDiaz-Vilchis, A. / Ruiz-Arellano, R.R. / Rosas-Benitez, E. / Rudino-Pinera, E.
Funding support Mexico, 1items
OrganizationGrant numberCountry
UNAMDGAPA IN 209114-3 Mexico
CitationJournal: To be Published
Title: Preserving metallic sites affected by radiation damage: the CuT2 case in Thermus thermophilus multicopper oxidase
Authors: Diaz-Vilchis, A. / Ruiz-Arellano, R.R. / Rosas-Benitez, E. / Stojanoff, V. / Rudino-Pinera, E.
History
DepositionMay 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: 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
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)50,51817
Polymers48,7911
Non-polymers1,72716
Water7,837435
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-117 kcal/mol
Surface area17300 Å2
Unit cell
Length a, b, c (Å)93.440, 109.860, 96.050
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-794-

HOH

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Components

#1: Protein Laccase / multicopper oxidase


Mass: 48791.457 Da / Num. of mol.: 1 / Fragment: UNP residues 24-462
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 (E. coli) / References: UniProt: Q72HW2, laccase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M HEPES, pH 7.5, 70% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 3, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.599→19.632 Å / Num. obs: 48075 / % possible obs: 99.8 % / Observed criterion σ(I): 3.24 / Redundancy: 4.53 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 19.11
Reflection shellResolution: 1.599→1.8 Å / Redundancy: 4.53 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 5.24 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2XU9

2xu9


Resolution: 1.599→19.632 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 15.91 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1755 2468 5.13 %
Rwork0.1496 45607 -
obs0.1509 48075 73.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.6 Å2 / Biso mean: 15.2806 Å2 / Biso min: 2.4 Å2
Refinement stepCycle: final / Resolution: 1.599→19.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 107 435 3981
Biso mean--36.26 27.09 -
Num. residues----439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054301
X-RAY DIFFRACTIONf_angle_d0.8815953
X-RAY DIFFRACTIONf_chiral_restr0.05651
X-RAY DIFFRACTIONf_plane_restr0.006795
X-RAY DIFFRACTIONf_dihedral_angle_d24.531689
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5995-1.63020.2491460.21782534268075
1.6302-1.66350.27011430.20642674281778
1.6635-1.69960.25021440.20012671281578
1.6996-1.73910.20741550.18432645280078
1.7391-1.78260.18241420.16712637277977
1.7826-1.83080.18931350.16122625276077
1.8308-1.88460.18691440.1612606275076
1.8846-1.94540.18391320.15022616274876
1.9454-2.01480.16941460.14482553269975
2.0148-2.09540.16771350.1422573270875
2.0954-2.19070.15381440.1392526267074
2.1907-2.3060.19911100.14192546265673
2.306-2.45020.20881310.14982503263473
2.4502-2.6390.20251350.1542442257771
2.639-2.90380.17131460.1472428257470
2.9038-3.32220.15551080.13322417252569
3.3222-4.1790.12431330.11922341247467
4.179-19.63370.14341390.14232270240963

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