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- PDB-6aje: Crystal structure of DHODH in complex with ferulenol from Eimeria... -

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Basic information

Entry
Database: PDB / ID: 6aje
TitleCrystal structure of DHODH in complex with ferulenol from Eimeria tenella
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrial
KeywordsMEMBRANE PROTEIN / Coccidium / mitochondria / electron transport chain / dihydroorotate dehydrogenase
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 signature 2. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / 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
Chem-9AU / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesEimeria tenella (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 Å
AuthorsShiba, T. / Inaoka, D.K. / Sato, D. / Hartuti, E.D. / Amalia, E. / Nagahama, M. / Yoshioka, Y. / Matsubayashi, M. / Balogun, E.O. / Tsuji, N. ...Shiba, T. / Inaoka, D.K. / Sato, D. / Hartuti, E.D. / Amalia, E. / Nagahama, M. / Yoshioka, Y. / Matsubayashi, M. / Balogun, E.O. / Tsuji, N. / Kita, K. / Harada, S.
CitationJournal: Genes (Basel) / Year: 2020
Title: Structural and Biochemical Features of Eimeria tenella Dihydroorotate Dehydrogenase, a Potential Drug Target.
Authors: Sato, D. / Hartuti, E.D. / Inaoka, D.K. / Sakura, T. / Amalia, E. / Nagahama, M. / Yoshioka, Y. / Tsuji, N. / Nozaki, T. / Kita, K. / Harada, S. / Matsubayashi, M. / Shiba, T.
History
DepositionAug 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase (quinone), mitochondrial
B: Dihydroorotate dehydrogenase (quinone), mitochondrial
C: Dihydroorotate dehydrogenase (quinone), mitochondrial
D: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,08416
Polymers195,1694
Non-polymers3,91612
Water00
1
A: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7714
Polymers48,7921
Non-polymers9793
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-5 kcal/mol
Surface area16530 Å2
MethodPISA
2
B: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7714
Polymers48,7921
Non-polymers9793
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-6 kcal/mol
Surface area16370 Å2
MethodPISA
3
C: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7714
Polymers48,7921
Non-polymers9793
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-6 kcal/mol
Surface area16690 Å2
MethodPISA
4
D: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7714
Polymers48,7921
Non-polymers9793
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-5 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.984, 132.984, 214.998
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Dihydroorotate dehydrogenase (quinone), mitochondrial / DHOdehase


Mass: 48792.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eimeria tenella (eukaryote) / Gene: ETH_00004975 / Plasmid: pET-19b / Production host: Escherichia coli (E. coli)
References: UniProt: U6KL66, dihydroorotate dehydrogenase (quinone)
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C17H21N4O9P
#3: Chemical
ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Chemical
ChemComp-9AU / 4-oxidanyl-3-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienyl]chromen-2-one


Mass: 366.493 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H30O3
Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES, 1.8 M Triammonium citrate, 1 mM ferulenol
PH range: 7.0-7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.65→50 Å / Num. obs: 24158 / % possible obs: 96.1 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 7.9
Reflection shellResolution: 3.65→3.71 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 1187 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AJ5

6aj5


Resolution: 3.65→20 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.767 / SU B: 96.038 / SU ML: 0.684 / Cross valid method: THROUGHOUT / ESU R Free: 0.874 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30334 1089 4.9 %RANDOM
Rwork0.22104 ---
obs0.22508 21056 92.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 61.906 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å2-0.51 Å20 Å2
2---1.01 Å20 Å2
3---3.28 Å2
Refinement stepCycle: 1 / Resolution: 3.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11764 0 276 0 12040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01912267
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211982
X-RAY DIFFRACTIONr_angle_refined_deg1.5222.00616595
X-RAY DIFFRACTIONr_angle_other_deg1.03327543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.93451498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.89423.578545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.687152159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.84515113
X-RAY DIFFRACTIONr_chiral_restr0.0970.21838
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113711
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022702
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0423.9296016
X-RAY DIFFRACTIONr_mcbond_other1.0413.9286015
X-RAY DIFFRACTIONr_mcangle_it1.9045.8837506
X-RAY DIFFRACTIONr_mcangle_other1.9045.8847507
X-RAY DIFFRACTIONr_scbond_it0.6974.0666251
X-RAY DIFFRACTIONr_scbond_other0.6974.0666252
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3736.0789090
X-RAY DIFFRACTIONr_long_range_B_refined4.03331.75714452
X-RAY DIFFRACTIONr_long_range_B_other4.03231.75914453
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.65→3.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 65 -
Rwork0.316 1026 -
obs--63.76 %
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)
11.32240.17980.0822.11930.2580.27860.1070.12310.09590.0735-0.053-0.1595-0.10580.0146-0.0540.3685-0.06550.0560.28910.00250.031212.8684-129.8474174.8159
21.27460.6010.61521.31520.09321.163-0.09350.1477-0.0215-0.02130.05880.125-0.01950.19230.03470.31980.0383-0.0150.1575-0.10010.121823.0789-103.9673204.0297
30.6807-0.35580.26681.20770.28691.60720.06810.0324-0.12180.2952-0.08270.1535-0.02680.24910.01460.3484-0.06030.04430.27550.04840.049146.6824-136.6839140.6698
40.7916-0.13030.18970.95050.19021.1339-0.0304-0.09550.3068-0.1546-0.18570.0204-0.195-0.04550.21610.36890.1107-0.04230.083-0.08540.282618.3862-108.0783116.2265
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 501
2X-RAY DIFFRACTION2B37 - 501
3X-RAY DIFFRACTION3C37 - 501
4X-RAY DIFFRACTION4D37 - 501

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