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- PDB-6uy4: Crystal structure of dihydroorotate dehydrogenase from Schistosom... -

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Basic information

Entry
Database: PDB / ID: 6uy4
TitleCrystal structure of dihydroorotate dehydrogenase from Schistosoma mansoni
ComponentsDihydroorotate dehydrogenase
KeywordsOXIDOREDUCTASE/INHIBITOR / SmDHODH / class 2 dihydroorotate dehydrogenase / Schistosoma mansoni / FLAVOPROTEIN / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase (quinone) activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane / nucleotide binding
Similarity search - Function
Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-QLA / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.796 Å
AuthorsMori, R.M. / Zapata, L.C.C. / Nonato, M.C.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2019/04395-6 Brazil
Sao Paulo Research Foundation (FAPESP)2019/08376-6 Brazil
CitationJournal: Febs J. / Year: 2021
Title: Structural basis for the function and inhibition of dihydroorotate dehydrogenase from Schistosoma mansoni.
Authors: de Mori, R.M. / Aleixo, M.A.A. / Zapata, L.C.C. / Calil, F.A. / Emery, F.S. / Nonato, M.C.
History
DepositionNov 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 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

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4507
Polymers41,3421
Non-polymers1,1086
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)187.981, 187.981, 187.981
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432

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Components

#1: Protein Dihydroorotate dehydrogenase


Mass: 41342.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_078730 / Plasmid: pET28a-SUMO / Details (production host): pET28a modified vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL
References: UniProt: G4VFD7, dihydroorotate dehydrogenase (fumarate)
#2: Chemical ChemComp-QLA / 2-[(4-fluorophenyl)amino]-3-hydroxynaphthalene-1,4-dione


Mass: 283.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H10FNO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.45 Å3/Da / Density % sol: 64.4 % / Description: Yellow cube
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 MES pH 6.5; 1.4 M CITRIC ACID

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 26, 2019
RadiationMonochromator: Cryogenically colled channel cut crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.796→47 Å / Num. obs: 14354 / % possible obs: 99.83 % / Redundancy: 39.8 % / CC1/2: 0.997 / Net I/σ(I): 15.2
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 2047 / CC1/2: 0.404

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UOY

6uoy
PDB Unreleased entry


Resolution: 2.796→46.995 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 707 4.94 %
Rwork0.2159 13601 -
obs0.2174 14308 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.68 Å2 / Biso mean: 79.8748 Å2 / Biso min: 51.19 Å2
Refinement stepCycle: final / Resolution: 2.796→46.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2617 0 76 45 2738
Biso mean--88.73 76.06 -
Num. residues----354
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.796-3.01190.41221270.3456263098
3.0119-3.31490.31241430.27052679100
3.3149-3.79440.27921410.2232688100
3.7944-4.77980.21561440.19012730100
4.7798-46.9950.21971520.20162874100

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