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- PDB-8r2u: Crystal structure of hydroquinone-2-hydroxylase from Trametes ver... -

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Basic information

Entry
Database: PDB / ID: 8r2u
TitleCrystal structure of hydroquinone-2-hydroxylase from Trametes versicolor (TvMNX3)
ComponentsPhenol 2-monooxygenase
KeywordsOXIDOREDUCTASE / fungi / hydroquinone / hydroxylase
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesTrametes versicolor (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsZahn, M. / Kuatsjah, E. / Salvachua, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)Research England E3 United Kingdom
CitationJournal: To Be Published
Title: Biochemical and structural characterization hydroquinone catabolic pathway from white-rot fungi
Authors: Schwartz, A. / Kuatsjah, E. / Zahn, M. / Salvachua, D.
History
DepositionNov 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenol 2-monooxygenase
B: Phenol 2-monooxygenase
C: Phenol 2-monooxygenase
D: Phenol 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,9908
Polymers275,8474
Non-polymers3,1424
Water7,584421
1
A: Phenol 2-monooxygenase
C: Phenol 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,4954
Polymers137,9242
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phenol 2-monooxygenase
D: Phenol 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,4954
Polymers137,9242
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.169, 178.193, 124.721
Angle α, β, γ (deg.)90.000, 129.301, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A

NCS domain segments:

Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 5 - 606 / Label seq-ID: 5 - 606

Dom-IDComponent-IDEns-ID
111
211
322
422
533
633
744
844
955
1055
1166
1266

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

#1: Protein
Phenol 2-monooxygenase


Mass: 68961.828 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes versicolor (fungus) / Gene: TRAPUB_13730 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Structure Screen 1+2 from Molecular Dimensions condition E12 (10 % PEG 6000, 5% MPD, 0.1 M HEPES pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.408→107.884 Å / Num. obs: 78277 / % possible obs: 92.4 % / Redundancy: 5.2 % / CC1/2: 0.973 / Rmerge(I) obs: 0.28 / Rpim(I) all: 0.134 / Net I/σ(I): 4.1
Reflection shellResolution: 2.408→2.595 Å / Redundancy: 5 % / Rmerge(I) obs: 0.951 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3915 / CC1/2: 0.648 / Rpim(I) all: 0.464 / % possible all: 73

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→107.884 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.887 / SU B: 23.223 / SU ML: 0.248 / Cross valid method: FREE R-VALUE / ESU R Free: 0.32
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2255 3986 5.093 %
Rwork0.1918 74278 -
all0.194 --
obs-78264 68.732 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.309 Å2
Baniso -1Baniso -2Baniso -3
1--0.863 Å20 Å2-0.405 Å2
2--1.032 Å2-0 Å2
3---0.211 Å2
Refinement stepCycle: LAST / Resolution: 2.41→107.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18676 0 212 421 19309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01219381
X-RAY DIFFRACTIONr_bond_other_d0.0010.01618035
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.64926365
X-RAY DIFFRACTIONr_angle_other_deg0.4791.57741506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12152410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.1385144
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.0654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.936103066
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.87410891
X-RAY DIFFRACTIONr_chiral_restr0.0650.22875
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222929
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024479
X-RAY DIFFRACTIONr_nbd_refined0.2110.23722
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.216783
X-RAY DIFFRACTIONr_nbtor_refined0.1820.29500
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.210376
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2554
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.040.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2690.229
X-RAY DIFFRACTIONr_nbd_other0.1920.2105
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.25
X-RAY DIFFRACTIONr_mcbond_it1.7611.5399634
X-RAY DIFFRACTIONr_mcbond_other1.7611.5399634
X-RAY DIFFRACTIONr_mcangle_it2.9812.75912037
X-RAY DIFFRACTIONr_mcangle_other2.9812.7612038
X-RAY DIFFRACTIONr_scbond_it2.2471.7789747
X-RAY DIFFRACTIONr_scbond_other2.2421.7789744
X-RAY DIFFRACTIONr_scangle_it3.7583.18914325
X-RAY DIFFRACTIONr_scangle_other3.7583.1914326
X-RAY DIFFRACTIONr_lrange_it6.16517.55921506
X-RAY DIFFRACTIONr_lrange_other6.16517.56721490
X-RAY DIFFRACTIONr_ncsr_local_group_10.0640.0519364
X-RAY DIFFRACTIONr_ncsr_local_group_20.0590.0519428
X-RAY DIFFRACTIONr_ncsr_local_group_30.0570.0519524
X-RAY DIFFRACTIONr_ncsr_local_group_40.0630.0519463
X-RAY DIFFRACTIONr_ncsr_local_group_50.0680.0519344
X-RAY DIFFRACTIONr_ncsr_local_group_60.0650.0519398
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.064150.0501
12AX-RAY DIFFRACTIONLocal ncs0.064150.0501
23AX-RAY DIFFRACTIONLocal ncs0.059070.0501
24AX-RAY DIFFRACTIONLocal ncs0.059070.0501
35AX-RAY DIFFRACTIONLocal ncs0.057190.0501
36AX-RAY DIFFRACTIONLocal ncs0.057190.0501
47AX-RAY DIFFRACTIONLocal ncs0.06290.0501
48AX-RAY DIFFRACTIONLocal ncs0.06290.0501
59AX-RAY DIFFRACTIONLocal ncs0.068250.0501
510AX-RAY DIFFRACTIONLocal ncs0.068250.0501
611AX-RAY DIFFRACTIONLocal ncs0.064670.0501
612AX-RAY DIFFRACTIONLocal ncs0.064670.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.41-2.4730.349420.2856870.28983710.9290.9468.70860.284
2.473-2.540.347740.27414380.27782080.9260.95418.42110.268
2.54-2.6140.3451090.27621500.27979430.920.95228.44010.27
2.614-2.6940.2931360.25926630.2677370.9510.95936.17680.252
2.694-2.7830.2861380.26831980.26974970.9420.95544.49780.26
2.783-2.880.2822100.24937700.2572270.9520.96455.07130.238
2.88-2.9890.2862740.24346520.24570370.9490.96370.00140.229
2.989-3.1110.282950.24354570.24567190.9480.96185.6080.228
3.111-3.2490.2723450.23160300.23364520.950.96698.80660.217
3.249-3.4070.2543470.21858190.2261700.9580.97199.93520.204
3.407-3.5920.2192720.256220.20158970.9710.97699.94910.19
3.592-3.8090.2182650.18853030.18955700.970.97999.96410.18
3.809-4.0720.2132770.17349470.17552350.9730.98299.78990.167
4.072-4.3970.1962630.15346250.15548890.9760.98699.97950.151
4.397-4.8160.172240.14442560.14544850.9820.98999.88850.145
4.816-5.3840.1761980.14338590.14540570.9820.9891000.144
5.384-6.2140.1851930.14434100.14636040.980.98999.97230.141
6.214-7.6040.161510.1428760.14130280.9860.98899.9670.14
7.604-10.7270.1551040.12222610.12423650.9850.9911000.133
10.727-107.8840.244690.25712530.25713450.9640.95698.290.294
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.54570.06910.09630.6301-0.05330.9124-0.016-0.06510.09190.00840.0022-0.0669-0.12130.03070.01370.06070.01150.03280.0152-0.00070.0537-5.66950.462248.6081
20.7504-0.1405-0.05260.5125-0.1730.6765-0.0237-0.02710.1460.05170.0044-0.0618-0.09350.0980.01930.0971-0.020.03040.017-0.00680.051342.2835-1.94498.8649
30.4965-0.07570.08670.6115-0.06830.89020.05110.0264-0.1426-0.0133-0.00860.03430.171-0.0638-0.04260.0747-0.01210.01650.011-0.00230.0801-4.987-40.908151.1361
40.694-0.0786-0.07390.70590.11310.54230.00660.0377-0.10820.00980.00070.01350.0843-0.0203-0.00740.07960.00910.02480.00730.00440.038545.0832-43.36310.2007
Refinement TLS groupSelection: ALL

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