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- PDB-8r2x: Crystal structure of hydroxyquinol-1,2-dioxygenase from Rhodococc... -

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Basic information

Entry
Database: PDB / ID: 8r2x
TitleCrystal structure of hydroxyquinol-1,2-dioxygenase from Rhodococcus jostii RHA1 (RjTsdC)
Components6-chlorohydroxyquinol-1,2-dioxygenase
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 dioxygenases signature. / : / Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core / Dioxygenase
Similarity search - Domain/homology
: / PHOSPHATIDYLETHANOLAMINE / 6-chlorohydroxyquinol-1,2-dioxygenase
Similarity search - Component
Biological speciesRhodococcus jostii RHA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.573 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: 6-chlorohydroxyquinol-1,2-dioxygenase
B: 6-chlorohydroxyquinol-1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2206
Polymers66,6402
Non-polymers1,5804
Water6,197344
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10300 Å2
ΔGint-107 kcal/mol
Surface area22040 Å2
Unit cell
Length a, b, c (Å)44.610, 107.411, 117.814
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: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 3 - 279 / Label seq-ID: 23 - 299

Dom-ID
1
2

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

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Components

#1: Protein 6-chlorohydroxyquinol-1,2-dioxygenase


Mass: 33319.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii RHA1 (bacteria) / Gene: tcpC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0SFL8
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PACT screen from Molecular Dimensions condition C10 (20% PEG 6000, 0.2 M magnesium chloride, 0.1 M HEPES pH 7.0)

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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: 1.573→79.375 Å / Num. obs: 42534 / % possible obs: 89.5 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.042 / Net I/σ(I): 12.3
Reflection shellResolution: 1.573→1.764 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.581 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2127 / CC1/2: 0.603 / Rpim(I) all: 0.484 / % possible all: 76.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.573→79.375 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.207 / WRfactor Rwork: 0.164 / SU B: 5.148 / SU ML: 0.09 / Average fsc free: 0.9601 / Average fsc work: 0.9735 / Cross valid method: FREE R-VALUE / ESU R: 0.171 / ESU R Free: 0.155
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2279 2165 5.09 %
Rwork0.1825 40369 -
all0.185 --
obs-42534 53.517 %
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: 22.895 Å2
Baniso -1Baniso -2Baniso -3
1-0.149 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.139 Å2
Refinement stepCycle: LAST / Resolution: 1.573→79.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4320 0 102 344 4766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124533
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164152
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.6586144
X-RAY DIFFRACTIONr_angle_other_deg0.521.5749565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8125556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.236542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31810673
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.77110231
X-RAY DIFFRACTIONr_chiral_restr0.070.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025422
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021078
X-RAY DIFFRACTIONr_nbd_refined0.2170.2927
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.23944
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22245
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22497
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2313
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0780.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0580.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.219
X-RAY DIFFRACTIONr_nbd_other0.2230.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.216
X-RAY DIFFRACTIONr_mcbond_it1.9231.682218
X-RAY DIFFRACTIONr_mcbond_other1.9241.682218
X-RAY DIFFRACTIONr_mcangle_it3.2023.0072770
X-RAY DIFFRACTIONr_mcangle_other3.2023.0072771
X-RAY DIFFRACTIONr_scbond_it2.7912.0722315
X-RAY DIFFRACTIONr_scbond_other2.7912.0742316
X-RAY DIFFRACTIONr_scangle_it4.4783.6653372
X-RAY DIFFRACTIONr_scangle_other4.4783.6663373
X-RAY DIFFRACTIONr_lrange_it6.84919.6165182
X-RAY DIFFRACTIONr_lrange_other6.81818.8855114
X-RAY DIFFRACTIONr_ncsr_local_group_10.0840.058853
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.083840.05009
12AX-RAY DIFFRACTIONLocal ncs0.083840.05009
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
1.573-1.6140.241110.2752090.27457890.9250.9283.80030.254
1.614-1.6580.369190.2733130.27956770.8440.9375.84820.256
1.658-1.7060.294360.2615510.26355050.9370.94510.6630.243
1.706-1.7590.346440.2578400.26153150.9170.94716.63220.234
1.759-1.8170.29630.23412500.23752010.9410.95625.24510.204
1.817-1.880.276830.23316790.23550230.9310.95835.07860.202
1.88-1.9510.2681060.2219980.22248530.9520.96643.35460.186
1.951-2.0310.2281170.21123620.21246960.9620.96952.78960.171
2.031-2.1210.247990.19719850.19945070.960.97346.23920.156
2.121-2.2250.241550.20231720.20342780.9640.97277.770.163
2.225-2.3450.2611540.20128020.20441150.9560.9771.83470.155
2.345-2.4870.241920.19736730.19938720.9590.97399.81920.153
2.487-2.6580.2422140.18534460.18936600.9630.9781000.15
2.658-2.8710.2331610.16432380.16733990.9670.9831000.138
2.871-3.1450.2321700.17130260.17431960.9670.9811000.148
3.145-3.5150.2191320.16727400.1728720.970.9821000.152
3.515-4.0580.1951170.16224450.16325620.9750.9841000.154
4.058-4.9670.21320.15320530.15621850.9790.9861000.155
4.967-7.010.2191030.19716160.19817190.9750.981000.195
7.01-79.3750.223570.2039710.20410330.9580.96999.5160.212
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)
10.36530.07060.510.57370.61621.4211-0.02030.02180.0107-0.01860.022-0.0306-0.06150.0701-0.00170.0071-0.00110.00470.00590.00460.011-4.2244-3.2832-0.4101
20.34320.02590.04321.10770.50650.74070.01140.0261-0.0696-0.0703-0.0327-0.03090.06170.01150.02130.02270.00450.0040.0273-0.00020.0358-12.7322-27.0029-26.9525
Refinement TLS groupSelection: ALL

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