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- PDB-5k5k: Crystal structure of laccasse from Thermus thermophilus HB27 (asc... -

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Basic information

Entry
Database: PDB / ID: 5k5k
TitleCrystal structure of laccasse from Thermus thermophilus HB27 (ascorbic acid 10 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: 1.796 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 23, 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)50,40016
Polymers48,7911
Non-polymers1,60915
Water5,981332
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-104 kcal/mol
Surface area17520 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


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.: 12 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 1.796→19.632 Å / Num. obs: 42011 / % possible obs: 91.2 % / Observed criterion σ(I): 3.66 / Redundancy: 2.45 % / Biso Wilson estimate: 13.63 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.83
Reflection shellResolution: 1.796→1.9 Å / Redundancy: 2.39 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.02 / % possible all: 94

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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: 1.796→19.632 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.58 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2159 2153 5.12 %
Rwork0.1752 39858 -
obs0.1773 42011 90.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.87 Å2 / Biso mean: 20.1967 Å2 / Biso min: 2.91 Å2
Refinement stepCycle: final / Resolution: 1.796→19.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 99 332 3870
Biso mean--56.13 31.79 -
Num. residues----437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064298
X-RAY DIFFRACTIONf_angle_d0.9375952
X-RAY DIFFRACTIONf_chiral_restr0.053651
X-RAY DIFFRACTIONf_plane_restr0.006798
X-RAY DIFFRACTIONf_dihedral_angle_d24.831687
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7955-1.83730.33971180.28192463258184
1.8373-1.88320.34561550.27462722287794
1.8832-1.93410.29531410.26412705284694
1.9341-1.99090.2841460.23572723286994
1.9909-2.05510.28161480.21942710285893
2.0551-2.12850.26411380.20342710284892
2.1285-2.21360.21851360.18612698283493
2.2136-2.31420.22611480.17942673282192
2.3142-2.4360.21161700.17352660283092
2.436-2.58830.22511520.17392685283792
2.5883-2.78760.23221390.16492668280791
2.7876-3.06720.20391460.1542648279490
3.0672-3.50890.18161290.1422653278290
3.5089-4.41250.14791430.12292612275587
4.4125-19.63340.16311440.1452528267282

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