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- PDB-3c3n: Crystal structure of dihydroorotate dehydrogenase from Trypanosom... -

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Basic information

Entry
Database: PDB / ID: 3c3n
TitleCrystal structure of dihydroorotate dehydrogenase from Trypanosoma cruzi strain Y
ComponentsDihydroorotate dehydrogenase
KeywordsOXIDOREDUCTASE / DHODH / Trypanosoma cruzi strain Y / dihydroorotate dehydrogenase / pyrd
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
FLAVIN MONONUCLEOTIDE / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsPinheiro, M.P. / Iulek, J. / Nonato, M.C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase from Y strain
Authors: Pinheiro, M.P. / Iulek, J. / Cristina Nonato, M.
History
DepositionJan 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase
B: Dihydroorotate dehydrogenase
C: Dihydroorotate dehydrogenase
D: Dihydroorotate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,22217
Polymers135,5524
Non-polymers2,67013
Water14,322795
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17280 Å2
ΔGint-179.7 kcal/mol
Surface area36700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.390, 123.920, 128.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Dihydroorotate dehydrogenase /


Mass: 33888.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: Y / Gene: tcdhod2 / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q4D3W2
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 795 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.5M ammonium sulfate, 5% v/v 2-Propanol, 0.1M sodium acetate, pH 5.0, 2mM Dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 7, 2006
RadiationMonochromator: Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
Reflection twinType: hemihedral / Operator: -h,-l,-k / Fraction: 0.091
ReflectionResolution: 2.2→55.8 Å / Num. all: 67674 / Num. obs: 62549 / % possible obs: 96.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 18.76 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 9.72
Reflection shellResolution: 2.2→2.23 Å / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 4.3 / Num. measured obs: 6600 / Num. unique obs: 2062 / % possible all: 77.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→55.8 Å / σ(F): 2828 / Stereochemistry target values: Engh & Huber
Details: Data twinning twinning operator: -h,-l,-k twinning fraction: 0.091
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3053 4.5 %twin related reflections are part of the same set
Rwork0.206 ---
obs0.207 62549 92.4 %-
all-67674 --
Solvent computationBsol: 59.827 Å2
Displacement parametersBiso mean: 15.299 Å2
Baniso -1Baniso -2Baniso -3
1--0.553 Å20 Å20 Å2
2---1.241 Å20 Å2
3---1.794 Å2
Refinement stepCycle: LAST / Resolution: 2.2→55.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9468 0 174 795 10437
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0441.5
X-RAY DIFFRACTIONc_scbond_it1.5132
X-RAY DIFFRACTIONc_mcangle_it1.572
X-RAY DIFFRACTIONc_scangle_it2.0792.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ligantes_mato.param
X-RAY DIFFRACTION5260108_cis_peptide.param

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