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- PDB-5k7a: Crystal structure of laccase fron Thermus thermophilus HB27 (sodi... -

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Basic information

Entry
Database: PDB / ID: 5k7a
TitleCrystal structure of laccase fron Thermus thermophilus HB27 (sodium nitrate 1.5 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: 1.5 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 metalic 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 25, 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)50,75519
Polymers48,7911
Non-polymers1,96318
Water9,530529
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-133 kcal/mol
Surface area17610 Å2
Unit cell
Length a, b, c (Å)93.744, 110.332, 96.484
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-837-

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


Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.56 Å3/Da / Density % sol: 51.89 %
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: X4A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 3, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.5→19.719 Å / Num. obs: 79274 / % possible obs: 97.3 % / Observed criterion σ(I): 3.65 / Redundancy: 4.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.76
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 4.39 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 3.49 / % possible all: 86.7

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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: 1.5→19.719 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 18.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1909 3981 5.02 %
Rwork0.1676 75293 -
obs0.1688 79274 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.49 Å2 / Biso mean: 14.8381 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 1.5→19.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 123 529 4091
Biso mean--37.2 28.47 -
Num. residues----437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054351
X-RAY DIFFRACTIONf_angle_d0.9066029
X-RAY DIFFRACTIONf_chiral_restr0.076659
X-RAY DIFFRACTIONf_plane_restr0.005805
X-RAY DIFFRACTIONf_dihedral_angle_d24.2711710
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4999-1.51820.31241210.27792328244986
1.5182-1.53740.30181330.27162675280899
1.5374-1.55760.24971560.25152633278999
1.5576-1.5790.29281450.24162675282099
1.579-1.60150.23111390.22622647278699
1.6015-1.62540.24181280.22482683281199
1.6254-1.65080.25681220.22192697281999
1.6508-1.67780.21431470.21712676282399
1.6778-1.70680.26121190.21052671279099
1.7068-1.73780.21591460.20852666281299
1.7378-1.77120.22241490.19652698284799
1.7712-1.80730.21221430.18882674281799
1.8073-1.84660.22371360.183926792815100
1.8466-1.88950.21551260.18227182844100
1.8895-1.93670.19111320.17126822814100
1.9367-1.9890.17271360.162827032839100
1.989-2.04750.18791380.163127082846100
2.0475-2.11350.18391360.156527042840100
2.1135-2.1890.20471560.15527222878100
2.189-2.27650.19241550.150926752830100
2.2765-2.37990.18421490.150226962845100
2.3799-2.50520.17971660.155827182884100
2.5052-2.66180.16991660.156226922858100
2.6618-2.86670.19111300.150427622892100
2.8667-3.15420.16891560.140627292885100
3.1542-3.60810.15711660.133127272893100
3.6081-4.53670.12681510.118427752926100
4.5367-19.72030.16861340.15442880301499

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