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- PDB-5k3k: Crystal structure of laccase from Thermus thermophilus HB27 (CuSO... -

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Basic information

Entry
Database: PDB / ID: 5k3k
TitleCrystal structure of laccase from Thermus thermophilus HB27 (CuSO4, 20 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: 1.644 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 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 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)50,63718
Polymers48,7911
Non-polymers1,84517
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-115 kcal/mol
Surface area17470 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

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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: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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, hanging 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: 1.644→19.632 Å / Num. obs: 38351 / % possible obs: 99.5 % / Observed criterion σ(I): 3.66 / Redundancy: 4.54 % / Biso Wilson estimate: 11.15 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.95
Reflection shellResolution: 1.644→1.8 Å / Redundancy: 4.56 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.32 / % possible all: 99.4

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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: 1.644→19.632 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 19.38 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.21 1926 5.02 %
Rwork0.1617 36425 -
obs0.1641 38351 63.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.27 Å2 / Biso mean: 15.9591 Å2 / Biso min: 1.43 Å2
Refinement stepCycle: final / Resolution: 1.644→19.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 115 345 3899
Biso mean--49.07 25.2 -
Num. residues----438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054336
X-RAY DIFFRACTIONf_angle_d0.8796002
X-RAY DIFFRACTIONf_chiral_restr0.049654
X-RAY DIFFRACTIONf_plane_restr0.005803
X-RAY DIFFRACTIONf_dihedral_angle_d25.561705
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6437-1.68480.31121210.25642576269763
1.6848-1.73030.26681620.23652730289268
1.7303-1.78120.26591760.21922725290168
1.7812-1.83870.26671300.20532738286867
1.8387-1.90430.24211310.19212724285567
1.9043-1.98050.22571460.17972671281766
1.9805-2.07060.24391420.16912659280165
2.0706-2.17960.21641330.15872643277665
2.1796-2.31590.20041290.15762589271864
2.3159-2.49440.22041330.1592555268863
2.4944-2.74490.22031410.15782519266062
2.7449-3.14060.1821400.13892479261960
3.1406-3.95160.16381260.12492455258159
3.9516-19.63360.15731160.12812362247855

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