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- PDB-5xfv: Crystal structures of FMN-bound form of dihydroorotate dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 5xfv
TitleCrystal structures of FMN-bound form of dihydroorotate dehydrogenase from Trypanosoma brucei
ComponentsDihydroorotate dehydrogenase (fumarate)
KeywordsOXIDOREDUCTASE / Neglected Tropical Diseases Flavin Enzyme Pyrimidine metabolism
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 A; chain A, domain 2 / Dihydroorotate Dehydrogenase A, chain A, domain 2 / Dihydroorotate dehydrogenase, class 1A / Dihydroorotate dehydrogenase, class 1/ 2 / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / Roll ...Dihydroorotate Dehydrogenase A; chain A, domain 2 / Dihydroorotate Dehydrogenase A, chain A, domain 2 / Dihydroorotate dehydrogenase, class 1A / Dihydroorotate dehydrogenase, class 1/ 2 / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / MALONATE ION / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesTrypanosoma brucei brucei strain 927/4 GUTat10.1 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsKubota, T. / Tani, O. / Yamaguchi, T. / Namatame, I. / Sakashita, H. / Furukawa, K. / Yamasaki, K.
CitationJournal: FEBS Open Bio / Year: 2018
Title: Crystal structures of FMN-bound and FMN-free forms of dihydroorotate dehydrogenase fromTrypanosoma brucei.
Authors: Kubota, T. / Tani, O. / Yamaguchi, T. / Namatame, I. / Sakashita, H. / Furukawa, K. / Yamasaki, K.
History
DepositionApr 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)148,80319
Polymers145,8564
Non-polymers2,94815
Water13,547752
1
A: Dihydroorotate dehydrogenase (fumarate)
B: Dihydroorotate dehydrogenase (fumarate)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,45310
Polymers72,9282
Non-polymers1,5258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-23 kcal/mol
Surface area20860 Å2
MethodPISA
2
C: Dihydroorotate dehydrogenase (fumarate)
D: Dihydroorotate dehydrogenase (fumarate)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3519
Polymers72,9282
Non-polymers1,4237
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-24 kcal/mol
Surface area20830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.914, 146.979, 66.491
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-547-

HOH

21A-694-

HOH

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Components

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


Mass: 36463.898 Da / Num. of mol.: 4 / Mutation: A115V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei strain 927/4 GUTat10.1 (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb927.5.3830 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q57U83, dihydroorotate dehydrogenase (fumarate)
#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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 752 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: parallelepiped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Sodium Citrate buffer, 1.5-2.5 M Sodium Malonate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 128274 / % possible obs: 99 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.1
Reflection shellResolution: 1.8→1.83 Å / Mean I/σ(I) obs: 7.1 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B4G

2b4g


Resolution: 1.79→34.98 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19762 6376 5 %RANDOM
Rwork0.16596 ---
obs0.16753 120628 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.277 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.79→34.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9552 0 201 752 10505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0199962
X-RAY DIFFRACTIONr_bond_other_d00.029289
X-RAY DIFFRACTIONr_angle_refined_deg1.1812.00513490
X-RAY DIFFRACTIONr_angle_other_deg3.575321624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56351244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60424.3393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.741151658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7051544
X-RAY DIFFRACTIONr_chiral_restr0.0680.21492
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02110984
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021928
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_it0.9082.1264988
X-RAY DIFFRACTIONr_mcbond_other0.9072.1254987
X-RAY DIFFRACTIONr_mcangle_it1.5133.1836228
X-RAY DIFFRACTIONr_mcangle_other1.5133.1846229
X-RAY DIFFRACTIONr_scbond_it1.2842.3134971
X-RAY DIFFRACTIONr_scbond_other1.2832.3124969
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1093.47262
X-RAY DIFFRACTIONr_long_range_B_refined3.98626.51412024
X-RAY DIFFRACTIONr_long_range_B_other3.76125.93511736
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.795→1.841 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 430 -
Rwork0.216 8449 -
obs--94.84 %

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