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- PDB-6w2k: Crystal structure of laccase from Thermus thermophilus HB27 in re... -

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Basic information

Entry
Database: PDB / ID: 6w2k
TitleCrystal structure of laccase from Thermus thermophilus HB27 in reducing conditions (Na2,S2,O2, 20 min)
ComponentsLaccase
KeywordsMETAL BINDING PROTEIN / Oxidoreductase / reduced conditions / multi-copper oxidase
Function / homology
Function and homology information


hydroquinone:oxygen oxidoreductase activity / laccase / outer membrane-bounded periplasmic space / copper ion binding
Similarity search - Function
Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, type 1 / 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 / molecular replacement / Resolution: 2 Å
AuthorsMiranda-Blancas, R. / Rudino-Pinera, E.
CitationJournal: To Be Published
Title: Dynamic behavior of alpha-beta loop at laccase of Thermus thermophilus
Authors: Miranda-Blancas, R. / Rudino-Pinera, E.
History
DepositionMar 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 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

Downloads & links

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Assembly

Deposited unit
A: Laccase
B: Laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,46022
Polymers97,6972
Non-polymers1,76320
Water15,853880
1
A: Laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,93913
Polymers48,8491
Non-polymers1,09012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5219
Polymers48,8491
Non-polymers6728
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.250, 96.230, 72.290
Angle α, β, γ (deg.)90.000, 99.360, 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.: 2
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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cu
#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.: 880 / 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: 2.54 Å3/Da / Density % sol: 51.54 % / Description: Elongated hexagons
Crystal growTemperature: 277.15 K / Method: batch mode / pH: 8 / Details: 20 mM Tris pH8, 100 mM HEPES pH 7.5, 65% MPD / PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0781 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 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2→19.944 Å / Num. obs: 64577 / % possible obs: 99.91 % / Redundancy: 3.1 % / Biso Wilson estimate: 13.53 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.044 / Rrim(I) all: 0.0806 / Net I/σ(I): 16.54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.151.664.46240190.920.2395
2.15-2.31.666.06180230.95717.794.6
2.3-2.351.696.951730.970.1494.6
2.35-2.41.667.1246640.970.1495.1
2.4-2.451.677.7542220.9750.1395
2.45-2.51.687.939410.9760.1394.1
2.5-2.651.688.6399640.9830.11494.4
2.65-2.751.699.9455530.9830.10493.3
2.75-2.851.6911.6747580.9890.08693.4
2.85-31.713.659360.9920.07192.6
3-41.7120.08200850.9970.04590.3
4-61.7429.8199400.9980.0386.8
6-101.7628.7932840.9980.03187.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASER7.0.076phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XU9

2xu9


Resolution: 2→19.944 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1971 3209 4.97 %
Rwork0.1449 61354 -
obs0.1475 64563 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.41 Å2 / Biso mean: 17.4541 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 2→19.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6886 0 209 882 7977
Biso mean--46.01 27.82 -
Num. residues----878
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02990.23271370.19032690100
2.0299-2.06160.21821520.18172698100
2.0616-2.09530.25291660.17792676100
2.0953-2.13140.23241670.16412675100
2.1314-2.17010.22951370.17052684100
2.1701-2.21180.18741280.16142738100
2.2118-2.25690.24941210.1607274199
2.2569-2.30590.22261410.15632666100
2.3059-2.35950.2321250.15662746100
2.3595-2.41840.21311350.15612702100
2.4184-2.48360.21381330.1572271099
2.4836-2.55660.25281310.1614270099
2.5566-2.63890.2751400.1644268999
2.6389-2.7330.23281740.158265599
2.733-2.84210.22381280.1453269299
2.8421-2.97110.20151510.14264198
2.9711-3.12720.17271360.1335269898
3.1272-3.32230.17941500.1311263497
3.3223-3.57740.14851410.1295261196
3.5774-3.93490.14011430.1148257895
3.9349-4.49860.16161070.1093261394
4.4986-5.64640.16321340.1206255493
5.6464-19.940.16821320.1574256392

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