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- PDB-9vpz: Crystal structure of wild-type Trypanosoma brucei DHODH in FMN-re... -

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Basic information

Entry
Database: PDB / ID: 9vpz
TitleCrystal structure of wild-type Trypanosoma brucei DHODH in FMN-reduced, ligand-free form
ComponentsDihydroorotate dehydrogenase (fumarate)
KeywordsFLAVOPROTEIN / Ping-Pong Reaction Mechanism / Substrate/Product-enzyme interactions.
Function / homology
Function and homology information


dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / fumarate metabolic process / dihydroorotate dehydrogenase activity / glycosome / ciliary plasm / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / nucleoplasm / cytoplasm
Similarity search - Function
Dihydroorotate dehydrogenase, class 1A / Dihydroorotate dehydrogenase, class 1/ 2 / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-FNR / MALONATE ION / SULFUR DIOXIDE / SULFITE ION / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKubota, T. / Tani, O. / Yamasaki, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2025
Title: Structural Basis of Redox-Dependent Affinities of Dihydroorotate Dehydrogenase for Its Substrates and Products.
Authors: Tani, O. / Kubota, T. / Yamasaki, T. / Hirokawa, T. / Furukawa, K. / Yamasaki, K.
History
DepositionJul 4, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase (fumarate)
C: Dihydroorotate dehydrogenase (fumarate)
B: Dihydroorotate dehydrogenase (fumarate)
D: Dihydroorotate dehydrogenase (fumarate)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,42727
Polymers137,8954
Non-polymers3,53223
Water7,782432
1
A: Dihydroorotate dehydrogenase (fumarate)
B: Dihydroorotate dehydrogenase (fumarate)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,76514
Polymers68,9472
Non-polymers1,81712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-35 kcal/mol
Surface area20770 Å2
MethodPISA
2
C: Dihydroorotate dehydrogenase (fumarate)
D: Dihydroorotate dehydrogenase (fumarate)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,66313
Polymers68,9472
Non-polymers1,71511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-35 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.376, 146.632, 65.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-612-

HOH

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Components

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Protein , 1 types, 4 molecules ACBD

#1: Protein
Dihydroorotate dehydrogenase (fumarate) / DHOD / DHODase / DHOdehase / Dihydroorotate oxidase


Mass: 34473.656 Da / Num. of mol.: 4 / Mutation: A115V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb927.5.3830
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q57U83, dihydroorotate dehydrogenase (fumarate)

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Non-polymers , 5 types, 455 molecules

#2: Chemical
ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H23N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: C3H2O4
#4: Chemical
ChemComp-SO2 / SULFUR DIOXIDE


Mass: 64.064 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2S
#5: Chemical
ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.1 M malonate, 48 mM citrate. soaked into saturated dithionite (< 1min)

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 136532 / % possible obs: 100 % / Redundancy: 6.58 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 17.6
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.696 / Num. unique obs: 6772

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XFV

5xfv


Resolution: 1.75→48.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.508 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20245 6774 5 %RANDOM
Rwork0.18163 ---
obs0.18265 129678 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.888 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.75→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9552 0 229 432 10213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0129982
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169474
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.82513509
X-RAY DIFFRACTIONr_angle_other_deg0.4211.73121907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42851244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.194560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.841101660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.21500
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211456
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022152
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_it0.6892.1114988
X-RAY DIFFRACTIONr_mcbond_other0.6882.1114988
X-RAY DIFFRACTIONr_mcangle_it1.1833.7956228
X-RAY DIFFRACTIONr_mcangle_other1.1833.7956229
X-RAY DIFFRACTIONr_scbond_it0.9612.2574994
X-RAY DIFFRACTIONr_scbond_other0.962.2554986
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6154.0937278
X-RAY DIFFRACTIONr_long_range_B_refined2.5820.9711004
X-RAY DIFFRACTIONr_long_range_B_other2.53520.5510921
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å
RfactorNum. reflection% reflection
Rfree0.272 489 -
Rwork0.256 8930 -
obs--93.71 %

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