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

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Basic information

Entry
Database: PDB / ID: 6wcm
TitleCrystal structure of Laccase from Thermus thermophilus HB27 with an open conformation of beta-hairpin (Average deposited dose 15.50 MGy)
ComponentsLaccase
KeywordsOXIDOREDUCTASE / open conformation / multicopper oxidase / laccase
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 beta-hairpin loop at laccase of Thermus thermophilus at 1.7 angstroms resolution
Authors: Miranda-Blancas, R. / Rudino-Pinera, E.
History
DepositionMar 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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)49,2144
Polymers48,8491
Non-polymers3653
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Prteins were loaded in superdex 75 column and eluted with 120 mL 20 mM MES and 50 NaCl
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.436, 60.817, 76.235
Angle α, β, γ (deg.)90.000, 109.340, 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.: 329 / 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 %
Crystal growTemperature: 277.15 K / Method: microbatch / pH: 5.5
Details: 20% PEG 4000, 20% 2-propanol, 100 mM 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: 1.1949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2018 / Details: Sagittal focusing 2nd crystal horizontal focusing
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1949 Å / Relative weight: 1
ReflectionResolution: 1.7→39.24 Å / Num. obs: 51812 / % possible obs: 99.98 % / Redundancy: 1.9 % / Biso Wilson estimate: 20.59 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.0503 / Rpim(I) all: 0.0503 / Rrim(I) all: 0.071 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value
3.66-38.841.90.02716.953060.9960.0270.038
2.91-3.661.90.03514.452090.9940.0350.05
2.54-2.911.90.05710.451790.9870.0570.08
2.31-2.541.90.076851930.980.0760.107
2.14-2.311.90.1036.751620.9650.1030.146
2.02-2.141.80.146551580.9410.1460.207
1.91-2.021.80.2113.651750.8850.2980.211
1.83-1.911.80.3122.551460.7780.3120.441
1.76-1.831.80.451.851270.6220.450.635
1.7-1.761.30.6531.351440.4510.6530.924

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
PHASER7.0.076phasing
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): 1.35 / Phase error: 24.82
RfactorNum. reflection% reflection
Rfree0.2375 2608 5.03 %
Rwork0.1965 --
obs0.1986 51812 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.85 Å2 / Biso mean: 26.3766 Å2 / Biso min: 9.02 Å2
Refinement stepCycle: final / Resolution: 1.7→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3443 0 17 329 3789
Biso mean--33.89 33.98 -
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
1.7-1.730.31591430.321925762719
1.73-1.760.29851370.301125462683
1.76-1.80.33971330.292325932726
1.8-1.840.30951410.27625502691
1.84-1.880.3381360.258225852721
1.88-1.930.27651410.248925602701
1.93-1.980.31551350.221725822717
1.98-2.040.26791210.226726112732
2.04-2.110.24491530.220625662719
2.11-2.180.27291180.199525992717
2.18-2.270.24081390.195925862725
2.27-2.370.25581550.194125612716
2.37-2.50.28221380.197225832721
2.5-2.650.24151210.195126052726
2.65-2.860.23891250.193826022727
2.86-3.140.24761750.190925782753
3.14-3.60.21151240.18426222746
3.6-4.530.17681180.156226382756
4.53-39.240.18681550.163726612816

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