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- PDB-3w1p: Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogena... -

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Basic information

Entry
Database: PDB / ID: 3w1p
TitleCrystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with 5-ethenyl-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
ComponentsDihydroorotate dehydrogenase (fumarate)
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Rossmann Fold / Oxidoreductase / Dihydroorotate/orotate 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
Chem-ERO / FLAVIN MONONUCLEOTIDE / COBALT HEXAMMINE(III) / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsInaoka, D.K. / Iida, M. / Tabuchi, T. / Lee, N. / Matsuoka, S. / Shiba, T. / Sakamoto, K. / Suzuki, S. / Balogun, E.O. / Nara, T. ...Inaoka, D.K. / Iida, M. / Tabuchi, T. / Lee, N. / Matsuoka, S. / 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: Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with 5-ethenyl-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
Authors: Inaoka, D.K. / Iida, M. / Tabuchi, T. / Lee, N. / Matsuoka, S. / Shiba, T. / Sakamoto, K. / Suzuki, S. / Balogun, E.O. / Nara, T. / Aoki, T. / Inoue, M. / Honma, T. / Tanaka, A. / Harada, S. / Kita, K.
History
DepositionNov 19, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Oct 30, 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)70,12513
Polymers68,1342
Non-polymers1,99111
Water10,449580
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-41 kcal/mol
Surface area21370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.321, 71.907, 124.026
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, 591 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical ChemComp-ERO / 5-ethenyl-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid / 5-vinyl-orotic acid


Mass: 182.134 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6N2O4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 298 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 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 39546 / Num. obs: 37145 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 10.05 / Num. unique all: 4106 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3W1A

3w1a


Resolution: 2→35.84 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.67 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22744 1954 5 %RANDOM
Rwork0.17833 ---
all0.18081 37092 --
obs0.18081 37092 93.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.93 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2→35.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 131 580 5487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195008
X-RAY DIFFRACTIONr_bond_other_d0.0020.024782
X-RAY DIFFRACTIONr_angle_refined_deg1.9062.0136791
X-RAY DIFFRACTIONr_angle_other_deg0.934311018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3955624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30924.059202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23815808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6221526
X-RAY DIFFRACTIONr_chiral_restr0.1120.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021098
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 135 -
Rwork0.16 2765 -
obs--95.55 %

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