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- PDB-3w7n: Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in co... -

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Basic information

Entry
Database: PDB / ID: 3w7n
TitleStructure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with TT2-3-149
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-W7N / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.39 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 TT2-3-149
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
DepositionMar 2, 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

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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)71,01618
Polymers68,1342
Non-polymers2,88216
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9250 Å2
ΔGint-45 kcal/mol
Surface area21840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.743, 72.951, 129.553
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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, 218 molecules

#2: Chemical ChemComp-W7N / 5-(2-{6-[(2-hydroxyethyl)carbamoyl]naphthalen-2-yl}ethyl)-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid


Mass: 397.381 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19N3O6
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / 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.: 202 / 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: 2.35 Å3/Da / Density % sol: 47.64 % / Mosaicity: 1.974 °
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: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 18, 2011
RadiationMonochromator: SI(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 25442 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.106 / Χ2: 2.249 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.38-2.4240.4753.7612431.52399.3
2.42-2.4740.40712701.55100
2.47-2.5140.37212391.52299.7
2.51-2.5640.35512521.71299.9
2.56-2.6240.33812651.70299.8
2.62-2.6840.26912791.78100
2.68-2.7540.25412681.75799.9
2.75-2.8240.23312661.83899.9
2.82-2.94.10.20612721.96999.8
2.9-340.18412612.00199.8
3-3.1140.1612762.19699.7
3.11-3.2340.13312752.26899.5
3.23-3.383.90.11112842.61299.7
3.38-3.553.80.09512632.76899.4
3.55-3.783.80.08612852.95498.8
3.78-4.073.70.07512553.04298
4.07-4.483.60.06912843.35397.3
4.48-5.133.50.06412693.19197.4
5.13-6.463.70.07112892.95396.9
6.46-503.50.05613472.86894.3

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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: PDB ENTRY 3W7E

3w7e


Resolution: 2.39→46.82 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.197 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.575 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 1296 5.1 %RANDOM
Rwork0.184 ---
obs0.1876 25302 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.74 Å2 / Biso mean: 37.7417 Å2 / Biso min: 17.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.39→46.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 193 202 5171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195093
X-RAY DIFFRACTIONr_angle_refined_deg1.8932.0256895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6345626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.23824.089203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81515809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1861526
X-RAY DIFFRACTIONr_chiral_restr0.1150.2759
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213814
LS refinement shellResolution: 2.388→2.449 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 63 -
Rwork0.222 1277 -
all-1340 -
obs--70.38 %

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