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- PDB-6aj5: Crystal structure of ligand-free type DHODH from Eimeria tenella -

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Basic information

Entry
Database: PDB / ID: 6aj5
TitleCrystal structure of ligand-free type DHODH 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
FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesEimeria tenella (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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)197,61812
Polymers195,1694
Non-polymers2,4508
Water00
1
A: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4053
Polymers48,7921
Non-polymers6122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-5 kcal/mol
Surface area15310 Å2
MethodPISA
2
B: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4053
Polymers48,7921
Non-polymers6122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-5 kcal/mol
Surface area15450 Å2
MethodPISA
3
C: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4053
Polymers48,7921
Non-polymers6122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-5 kcal/mol
Surface area15810 Å2
MethodPISA
4
D: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4053
Polymers48,7921
Non-polymers6122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-5 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)248.808, 248.808, 248.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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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: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H4N2O4
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: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES, 3.0 M ammonium sulfate / 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: Nov 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 32346 / % possible obs: 100 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 5.6
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.62 / Num. unique obs: 1587 / % possible all: 100

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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: 3W7R

3w7r


Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.857 / Cor.coef. Fo:Fc free: 0.731 / SU B: 99.954 / SU ML: 0.692 / Cross valid method: THROUGHOUT / ESU R Free: 0.811 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35881 1493 4.8 %RANDOM
Rwork0.27177 ---
obs0.27586 29340 95.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.361 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11285 0 168 0 11453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911653
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211344
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.99115753
X-RAY DIFFRACTIONr_angle_other_deg1.13326075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.31451437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.30823.484531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.688152072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.87215115
X-RAY DIFFRACTIONr_chiral_restr0.0940.21752
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113062
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022581
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_it0.9322.3645772
X-RAY DIFFRACTIONr_mcbond_other0.9322.3645771
X-RAY DIFFRACTIONr_mcangle_it1.7313.5397201
X-RAY DIFFRACTIONr_mcangle_other1.7313.5397202
X-RAY DIFFRACTIONr_scbond_it0.5562.4955881
X-RAY DIFFRACTIONr_scbond_other0.5562.4955880
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0963.7068553
X-RAY DIFFRACTIONr_long_range_B_refined3.60118.89113660
X-RAY DIFFRACTIONr_long_range_B_other3.60118.89113661
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.501→3.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 74 -
Rwork0.325 1147 -
obs--52.11 %
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)
10.6507-0.0363-0.21051.1557-0.80451.52620.18170.03890.0169-0.0459-0.0463-0.10940.0812-0.1028-0.13530.24940.05050.04920.12060.15180.206628.7623251.1616287.0332
20.20480.12570.19341.7476-0.72161.55980.1064-0.1469-0.0209-0.0531-0.0415-0.1775-0.0428-0.152-0.06480.2022-0.1444-0.10070.19720.13490.23828.5835233.0624321.4066
30.15210.09180.46961.44250.7791.84190.06210.0954-0.0912-0.02550.06310.1519-0.07560.1887-0.12530.2230.1231-0.09260.1872-0.20910.285782.6664246.3121300.4359
40.25220.1021-0.47891.49970.691.47740.0062-0.0595-0.00430.0462-0.06280.1160.0740.11570.05660.1951-0.05950.12160.1469-0.19140.288682.7195264.4402334.6636
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 402
2X-RAY DIFFRACTION2B18 - 402
3X-RAY DIFFRACTION3C18 - 402
4X-RAY DIFFRACTION4D18 - 402

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