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- PDB-8r2v: Crystal structure of hydroxyquinol-1,2-dioxygenase from Gelatopor... -

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Basic information

Entry
Database: PDB / ID: 8r2v
TitleCrystal structure of hydroxyquinol-1,2-dioxygenase from Gelatoporia subvermispora (GsHDX1)
ComponentsIntradiol ring-cleavage dioxygenases domain-containing protein
KeywordsOXIDOREDUCTASE / fungi / hydroxyquinol / 1 / 2-dioxygenase
Function / homology
Function and homology information


catechol-containing compound metabolic process / catechol 1,2-dioxygenase activity / ferric iron binding
Similarity search - Function
Catechol dioxygenase, N-terminal / Catechol dioxygenase N terminus / : / Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core / Dioxygenase
Similarity search - Domain/homology
: / PHOSPHATIDYLETHANOLAMINE / Intradiol ring-cleavage dioxygenases domain-containing protein
Similarity search - Component
Biological speciesGelatoporia subvermispora (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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: Intradiol ring-cleavage dioxygenases domain-containing protein
B: Intradiol ring-cleavage dioxygenases domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,76115
Polymers77,3162
Non-polymers2,44413
Water9,422523
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15210 Å2
ΔGint-239 kcal/mol
Surface area26540 Å2
Unit cell
Length a, b, c (Å)48.433, 148.662, 157.746
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 4 - 322 / Label seq-ID: 4 - 322

Dom-ID
1
2

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

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Components

#1: Protein Intradiol ring-cleavage dioxygenases domain-containing protein


Mass: 38658.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gelatoporia subvermispora (fungus) / Gene: CERSUDRAFT_116134 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M2PH20
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 3.67 Å3/Da / Density % sol: 66.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Structure Screen 1+2 from Molecular Dimensions condition F11 (1.6 M ammonium sulfate, 10% 1,4-dioxane, 0.1 M MES 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: Jan 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.777→108.189 Å / Num. obs: 79137 / % possible obs: 94.5 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.049 / Net I/σ(I): 11
Reflection shellResolution: 1.777→1.971 Å / Redundancy: 14.5 % / Rmerge(I) obs: 1.942 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3957 / CC1/2: 0.638 / Rpim(I) all: 0.526 / % possible all: 67.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→108.189 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.231 / SU ML: 0.079 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1971 3939 4.978 %
Rwork0.1731 75197 -
all0.174 --
obs-79136 71.824 %
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: 29.612 Å2
Baniso -1Baniso -2Baniso -3
1--0.086 Å2-0 Å2-0 Å2
2---0.064 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.78→108.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4970 0 147 523 5640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125245
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164930
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.6627126
X-RAY DIFFRACTIONr_angle_other_deg0.4971.5711439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8555644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.915538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28110835
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.55410241
X-RAY DIFFRACTIONr_chiral_restr0.0710.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021110
X-RAY DIFFRACTIONr_nbd_refined0.2260.21064
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.24628
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22659
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2445
X-RAY DIFFRACTIONr_metal_ion_refined0.0760.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1690.210
X-RAY DIFFRACTIONr_nbd_other0.1620.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.230.215
X-RAY DIFFRACTIONr_mcbond_it1.9832.0812558
X-RAY DIFFRACTIONr_mcbond_other1.9822.0812558
X-RAY DIFFRACTIONr_mcangle_it2.9213.7183196
X-RAY DIFFRACTIONr_mcangle_other2.923.7213197
X-RAY DIFFRACTIONr_scbond_it4.0932.7232687
X-RAY DIFFRACTIONr_scbond_other3.9992.6962672
X-RAY DIFFRACTIONr_scangle_it6.1294.7343926
X-RAY DIFFRACTIONr_scangle_other6.0224.6853903
X-RAY DIFFRACTIONr_lrange_it8.22223.615981
X-RAY DIFFRACTIONr_lrange_other8.14322.9395855
X-RAY DIFFRACTIONr_ncsr_local_group_10.0640.0510064
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.064430.05009
12AX-RAY DIFFRACTIONLocal ncs0.064430.05009
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
1.78-1.8260.326120.2941620.29780200.9220.9262.16960.291
1.826-1.8760.35340.2727500.27578630.9090.9479.97070.264
1.876-1.9310.267660.26213720.26276660.9530.95418.75820.252
1.931-1.990.2581210.25423930.25473860.9590.95934.03740.237
1.99-2.0550.2761780.25837830.25971840.950.95755.13640.238
2.055-2.1270.2672750.2450940.24169680.9540.96377.05220.218
2.127-2.2080.2283480.22562410.22567530.9650.96797.57140.2
2.208-2.2980.2363590.21661360.21764950.9620.9691000.185
2.298-2.40.2113120.19359050.19462170.970.9761000.163
2.4-2.5170.1892780.17856810.17959590.9780.9811000.147
2.517-2.6530.2072560.17254180.17456740.9740.9831000.143
2.653-2.8140.1972780.16251230.16454010.9770.9841000.136
2.814-3.0080.2022320.16948670.1750990.9740.9831000.147
3.008-3.2490.1932530.16344800.16447330.9770.9831000.146
3.249-3.5590.1892380.1641220.16243600.9770.9851000.152
3.559-3.9780.1731860.15137970.15239830.9830.9871000.149
3.978-4.5920.1671810.13533650.13735460.9850.991000.142
4.592-5.6220.1661540.14428700.14530240.9860.9891000.155
5.622-7.940.1871100.1622930.16224030.9820.9861000.175
7.94-108.1890.177680.17113430.17214110.9810.9711000.195
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)
10.3701-0.3040.4290.742-0.93931.3872-0.0126-0.02410.09920.0180.0309-0.0186-0.0847-0.0431-0.01830.0526-0.01410.01430.02780.01380.06851.5644-2.3918-18.4256
20.4729-0.46140.41621.0924-0.93790.9934-0.0131-0.09380.01920.0298-0.0243-0.0432-0.0215-0.02450.03740.0336-0.00780.01340.0492-0.00130.0091-13.968519.0388-42.6734
Refinement TLS groupSelection: ALL

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