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- PDB-8r2w: Crystal structure of hydroxyquinol-1,2-dioxygenase from Trametes ... -

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Basic information

Entry
Database: PDB / ID: 8r2w
TitleCrystal structure of hydroxyquinol-1,2-dioxygenase from Trametes versicolor (TvHDX1)
ComponentsHydroxyquinol 1,2-dioxygenase
KeywordsOXIDOREDUCTASE / fungi / hydroxyquinol / 1 / 2-dioxygenase
Function / homology: / PHOSPHATIDYLETHANOLAMINE
Function and homology information
Biological speciesTrametes versicolor (turkey-tail fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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: Cell Rep / Year: 2024
Title: Biochemical and structural characterization of enzymes in the 4-hydroxybenzoate catabolic pathway of lignin-degrading white-rot fungi.
Authors: Kuatsjah, E. / Schwartz, A. / Zahn, M. / Tornesakis, K. / Kellermyer, Z.A. / Ingraham, M.A. / Woodworth, S.P. / Ramirez, K.J. / Cox, P.A. / Pickford, A.R. / Salvachua, D.
History
DepositionNov 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydroxyquinol 1,2-dioxygenase
B: Hydroxyquinol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0167
Polymers77,3142
Non-polymers1,7025
Water10,196566
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10780 Å2
ΔGint-107 kcal/mol
Surface area23260 Å2
Unit cell
Length a, b, c (Å)177.362, 54.118, 69.486
Angle α, β, γ (deg.)90.000, 108.385, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 20 - 309 / Label seq-ID: 20 - 309

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Hydroxyquinol 1,2-dioxygenase


Mass: 38657.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes versicolor (turkey-tail fungus)
Gene: TRAPUB_151 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PACT screen from Molecular Dimensions condition F2 (20 % PEG 3350, 0.2 M sodium bromide, 0.1 M Bis-Tris propane pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.459→84.155 Å / Num. obs: 87832 / % possible obs: 94.1 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Net I/σ(I): 14.2
Reflection shellResolution: 1.459→1.572 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.143 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4392 / CC1/2: 0.644 / Rpim(I) all: 0.468 / % possible all: 55

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→84.155 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.897 / SU ML: 0.056 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.081
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2029 4337 4.938 %
Rwork0.1717 83491 -
all0.173 --
obs-87828 80.806 %
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: 23.965 Å2
Baniso -1Baniso -2Baniso -3
1--0.093 Å2-0 Å20.152 Å2
2---0.123 Å2-0 Å2
3---0.095 Å2
Refinement stepCycle: LAST / Resolution: 1.46→84.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4546 0 110 566 5222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124782
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164497
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.6656484
X-RAY DIFFRACTIONr_angle_other_deg0.5031.57610418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.978537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64410754
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.56710220
X-RAY DIFFRACTIONr_chiral_restr0.0750.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025519
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021045
X-RAY DIFFRACTIONr_nbd_refined0.2220.2903
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.24085
X-RAY DIFFRACTIONr_nbtor_refined0.180.22321
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22544
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2396
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0650.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1280.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.216
X-RAY DIFFRACTIONr_nbd_other0.1470.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.249
X-RAY DIFFRACTIONr_mcbond_it1.8011.8532323
X-RAY DIFFRACTIONr_mcbond_other1.8021.8532322
X-RAY DIFFRACTIONr_mcangle_it2.5963.3222900
X-RAY DIFFRACTIONr_mcangle_other2.5953.3232901
X-RAY DIFFRACTIONr_scbond_it2.7952.1972459
X-RAY DIFFRACTIONr_scbond_other2.7952.1972460
X-RAY DIFFRACTIONr_scangle_it4.1623.8733582
X-RAY DIFFRACTIONr_scangle_other4.1613.8733583
X-RAY DIFFRACTIONr_lrange_it5.94521.2925402
X-RAY DIFFRACTIONr_lrange_other5.83520.1095259
X-RAY DIFFRACTIONr_ncsr_local_group_10.1080.058963
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.108370.05007
12AX-RAY DIFFRACTIONLocal ncs0.108370.05007
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
1.46-1.4980.299170.2732510.27479990.9480.9533.35040.27
1.498-1.5390.294640.27113790.27277910.9540.95218.52140.267
1.539-1.5840.2551720.2635340.2675690.9590.95548.96290.253
1.584-1.6320.2792530.24149310.24373770.9490.96270.27250.229
1.632-1.6860.2773070.23462010.23671410.9530.96491.13570.217
1.686-1.7450.2533750.21864840.2268960.9580.9799.46350.197
1.745-1.8110.2263190.20263370.20366560.9660.9741000.179
1.811-1.8850.2183040.18961070.1964110.9690.9781000.165
1.885-1.9680.2073000.17558640.17761640.9750.9811000.155
1.968-2.0640.2073010.17455820.17558830.9730.9821000.156
2.064-2.1760.1992970.16753360.16956370.9770.98399.9290.154
2.176-2.3080.1892670.16750330.16853060.9790.98399.88690.154
2.308-2.4670.2062610.15947150.16249770.9740.98599.97990.149
2.467-2.6650.1772320.15744440.15846760.9810.9851000.15
2.665-2.9190.22400.15940440.16142840.9760.9841000.155
2.919-3.2630.1942060.16536870.16738930.9790.9831000.166
3.263-3.7660.1791430.16233090.16334540.9810.98599.94210.172
3.766-4.6110.151330.14528060.14529410.9870.98899.9320.167
4.611-6.5110.229860.17622040.17822900.9820.9861000.206
6.511-84.1550.299600.19612420.213050.960.97499.77010.24
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.43870.21060.59460.48280.42851.41990.00440.0666-0.0554-0.02220.014-0.01880.0524-0.0016-0.01840.01650.00410.01360.0359-0.0070.023649.18991.672519.5703
20.50360.01820.21840.7810.52940.7906-0.0047-0.00630.00940.0479-0.0075-0.0171-0.00230.03170.01220.0078-0.0011-0.00060.00910.00620.00558.184923.028346.8183
Refinement TLS groupSelection: ALL

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