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- PDB-3w76: Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in co... -

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Basic information

Entry
Database: PDB / ID: 3w76
TitleStructure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-4-189
ComponentsDihydroorotate dehydrogenase (fumarate)
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Rossmann Fold / Oxidoreductase / Dihydroorotate/orotate and fumarate/succinate binding / Cytosol / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / 'de novo' UMP biosynthetic process / 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 / COBALT HEXAMMINE(III) / Chem-W76 / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsInaoka, D.K. / Iida, M. / Tabuchi, T. / Lee, N. / Hashimoto, S. / Matsuoka, S. / Kuranaga, T. / Shiba, T. / Sakamoto, K. / Suzuki, S. ...Inaoka, D.K. / Iida, M. / Tabuchi, T. / Lee, N. / Hashimoto, S. / Matsuoka, S. / Kuranaga, T. / Shiba, T. / Sakamoto, K. / Suzuki, S. / Balogun, E.O. / Nara, T. / Aoki, T. / Inoue, M. / Honma, T. / Tanaka, A. / Harada, S. / Kita, K.
CitationJournal: To be Published
Title: Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-4-189
Authors: Inaoka, D.K. / Iida, M. / Tabuchi, T. / Lee, N. / Hashimoto, S. / Matsuoka, S. / Kuranaga, T. / Shiba, T. / Sakamoto, K. / Suzuki, S. / Balogun, E.O. / Nara, T. / Aoki, T. / Inoue, M. / ...Authors: Inaoka, D.K. / Iida, M. / Tabuchi, T. / Lee, N. / Hashimoto, S. / Matsuoka, S. / Kuranaga, T. / Shiba, T. / Sakamoto, K. / Suzuki, S. / Balogun, E.O. / Nara, T. / Aoki, T. / Inoue, M. / Honma, T. / Tanaka, A. / Harada, S. / Kita, K.
History
DepositionFeb 27, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 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 (fumarate)
B: Dihydroorotate dehydrogenase (fumarate)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,17022
Polymers68,1342
Non-polymers3,03620
Water10,323573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-30 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.744, 71.694, 128.829
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 34067.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: CL Brener / Gene: PyrD / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q4D3W2, dihydroorotate dehydrogenase (fumarate)

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Non-polymers , 5 types, 593 molecules

#2: Chemical ChemComp-W76 / 5-[2-(3-methoxyphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid


Mass: 290.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14N2O5
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.42 % / Mosaicity: 0.628 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 0.1M Cacodylate, 13% PEG3350, 0.05M Hexaamminecobalt (III) Chloride, 1mM Oxonate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 86585 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.057 / Χ2: 1.624 / Net I/σ(I): 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.58-1.615.10.4224.5342971.475100
1.61-1.645.10.38442771.461100
1.64-1.675.10.32242791.487100
1.67-1.75.10.30142811.532100
1.7-1.745.10.26542931.534100
1.74-1.785.20.22342741.532100
1.78-1.825.20.18343021.536100
1.82-1.875.20.16342831.525100
1.87-1.935.20.12743071.54100
1.93-1.995.20.10943141.606100
1.99-2.065.20.08742861.577100
2.06-2.145.20.07443181.554100
2.14-2.245.20.06343451.569100
2.24-2.365.20.05842971.613100
2.36-2.515.20.05443521.76100
2.51-2.75.10.05243442.0599.9
2.7-2.975.10.0543582.30199.9
2.97-3.450.03944022.0599.8
3.4-4.2950.02544251.45899.7
4.29-5050.02345511.30898.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W1T

3w1t


Resolution: 1.58→31.32 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.111 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1705 4337 5 %RANDOM
Rwork0.1386 ---
obs0.1402 86502 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.47 Å2 / Biso mean: 16.0074 Å2 / Biso min: 6.35 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.58→31.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 201 573 5550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0195081
X-RAY DIFFRACTIONr_bond_other_d0.0030.024865
X-RAY DIFFRACTIONr_angle_refined_deg2.3242.0246874
X-RAY DIFFRACTIONr_angle_other_deg1.0563.00211214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3555626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64624.059202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92615812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6331526
X-RAY DIFFRACTIONr_chiral_restr0.1410.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0215640
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021102
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 361 -
Rwork0.18 5950 -
all-6311 -
obs--99.43 %

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