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- PDB-5ea9: Crystal Structure of Trypanosoma cruzi Dihydroorotate Dehydrogena... -

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Basic information

Entry
Database: PDB / ID: 5ea9
TitleCrystal Structure of Trypanosoma cruzi Dihydroorotate Dehydrogenase in Complex with Neq0130
ComponentsDihydroorotate dehydrogenase (fumarate)Dihydroorotate dehydrogenase (fumarate)
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / T. cruzi / Dihydroorotate Dehydrogenase / covalent inhibitor / 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 / TIM Barrel ...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-5LM / FLAVIN MONONUCLEOTIDE / COBALT HEXAMMINE(III) / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesTrypanosoma cruzi strain CL Brener (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.71 Å
AuthorsRocha, J.R. / Inaoka, D.K. / Cheleski, J. / Shiba, T. / Harada, S. / Montanari, C.A. / Kita, K.
Funding support Japan, Brazil, 4items
OrganizationGrant numberCountry
Creative Scientific Research18GS0314 Japan
Japanese Society for the Promotion of Science18073004, 26253025, 26870119 Japan
Science and Technology Research Partnership for Sustainable Development10000284 Japan
Fundacao de Amparo a Pesquisa do Estado de Sao Paulo2010/20021-4, 2012/01777-6 Brazil
CitationJournal: To be Published
Title: Exploring Trypanosoma cruzi Dihydroorotate Dehydrogenase Active Site Plasticity for the Discovery of Potent and Selective Inhibitors with Trypanocidal Activity
Authors: Rocha, J.R. / Cheleski, J. / Inaoka, D.K. / Avelar, L.A. / Ribeiro, J.F.R. / Wiggers, H.J. / Albuquerque, S. / Shiba, T. / Harada, S. / Kita, K. / Silva, A.B.F. / Montanari, C.A.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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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)71,92032
Polymers68,3092
Non-polymers3,61130
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-29 kcal/mol
Surface area22070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.284, 71.863, 124.264
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) / Dihydroorotate dehydrogenase (fumarate) / DHOdehase / Dihydroorotate oxidase


Mass: 34154.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: genetically manipulated
Source: (gene. exp.) Trypanosoma cruzi strain CL Brener (eukaryote)
Strain: CL Brener / Gene: PyrD,pyr4 / Plasmid: pET SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q4D3W2, dihydroorotate dehydrogenase (fumarate)

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Non-polymers , 6 types, 553 molecules

#2: Chemical ChemComp-5LM / 5-[(E)-3-thiophen-2-ylprop-2-enylidene]-1,3-diazinane-2,4,6-trione


Mass: 248.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H8N2O3S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 100 mM CACODILATE, 13% PEG3350, 50 mM HEXAMMINECOBALT (III) CHLORIDE, 5 mM OXONATE
PH range: 5.0-5.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 26, 2013
RadiationMonochromator: SI(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 7.2 % / Number: 484462 / Rmerge(I) obs: 0.064 / Χ2: 0.97 / D res high: 1.71 Å / D res low: 50 Å / Num. obs: 66881 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.645010.031.0316.7
3.684.6410.0291.0337.1
3.223.6810.0320.8837.3
2.923.2210.040.8567.3
2.712.9210.0470.8537.3
2.552.7110.0540.8637.3
2.432.5510.0640.8877.4
2.322.4310.0730.9067.4
2.232.3210.0820.9417.3
2.152.2310.090.9577.3
2.092.1510.1030.9747.3
2.032.0910.121.0177.3
1.972.0310.1371.0147.3
1.931.9710.1741.0247.3
1.881.9310.1981.0277.3
1.841.8810.2471.047.2
1.811.8410.2841.0457.2
1.771.8110.3171.0547.2
1.741.7710.3641.0347.1
1.711.7410.411.037.1
ReflectionResolution: 1.71→50 Å / Num. obs: 66881 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.064 / Χ2: 0.972 / Net I/av σ(I): 31.312 / Net I/σ(I): 8.6 / Num. measured all: 484462
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.71-1.747.10.4132561.0399.7
1.74-1.777.10.36433161.03499.9
1.77-1.817.20.31733041.05499.9
1.81-1.847.20.28432991.045100
1.84-1.887.20.24732841.04100
1.88-1.937.30.19833041.027100
1.93-1.977.30.17433131.024100
1.97-2.037.30.13733381.014100
2.03-2.097.30.1233351.017100
2.09-2.157.30.10333180.974100
2.15-2.237.30.0933020.957100
2.23-2.327.30.08233590.941100
2.32-2.437.40.07333290.906100
2.43-2.557.40.06433590.887100
2.55-2.717.30.05433520.863100
2.71-2.927.30.04733620.853100
2.92-3.227.30.0433810.856100
3.22-3.687.30.03234130.883100
3.68-4.647.10.02934211.03399.5
4.64-506.70.0335361.03197.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREPmodel building
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.294 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 3333 5 %RANDOM
Rwork0.179 ---
obs0.1811 63240 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.9 Å2 / Biso mean: 18.968 Å2 / Biso min: 4.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2---0.62 Å20 Å2
3---0.3 Å2
Refinement stepCycle: final / Resolution: 1.71→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 245 523 5544
Biso mean--25.87 27.57 -
Num. residues----626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0195142
X-RAY DIFFRACTIONr_bond_other_d0.0030.024962
X-RAY DIFFRACTIONr_angle_refined_deg2.3692.0286956
X-RAY DIFFRACTIONr_angle_other_deg1.214311427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8295636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15224.02204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58815818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2191527
X-RAY DIFFRACTIONr_chiral_restr0.1430.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215670
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021115
X-RAY DIFFRACTIONr_mcbond_it1.9761.6192517
X-RAY DIFFRACTIONr_mcbond_other1.951.6172516
X-RAY DIFFRACTIONr_mcangle_it2.7572.4183147
LS refinement shellResolution: 1.71→1.754 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 275 -
Rwork0.216 4528 -
all-4803 -
obs--98.83 %

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