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- PDB-2e6a: Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogena... -

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Basic information

Entry
Database: PDB / ID: 2e6a
TitleCrystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with orotate
ComponentsDihydroorotate dehydrogenase
KeywordsOXIDOREDUCTASE / Chagas disease / Pyrimidine Biosynthesis / Dihydroorotate Dehydrogenase / Fumarate Reductase / Energy Metabolism / Redox Homeostasis / Flavoprotein
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 / COBALT HEXAMMINE(III) / OROTIC ACID / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsInaoka, D.K. / Shimizu, H. / Sakamoto, K. / Shiba, T. / Kurisu, G. / Nara, T. / Aoki, T. / Harada, S. / Kita, K.
CitationJournal: To be Published
Title: Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with orotate
Authors: Inaoka, D.K. / Shimizu, H. / Sakamoto, K. / Shiba, T. / Kurisu, G. / Nara, T. / Aoki, T. / Harada, S. / Kita, K.
History
DepositionDec 26, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,15111
Polymers68,3972
Non-polymers1,7549
Water8,935496
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-33 kcal/mol
Surface area20850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.248, 71.881, 123.574
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 /


Mass: 34198.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: TALAHUEN / Gene: TCDHOD2 / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q4D3W2, EC: 1.3.3.1

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Non-polymers , 5 types, 505 molecules

#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-ORO / OROTIC ACID / Orotic acid


Mass: 156.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N2O4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 18% PEG 3350, 1mM Sodium orotate, 0.25M Hexammine cobalt trichloride, 0.1M cacodylate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Dec 20, 2003
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. all: 75068 / Num. obs: 72280 / % possible obs: 96.3 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.9
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.12 / Num. unique all: 7243 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DOR

2dor


Resolution: 1.64→49.51 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.477 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.093 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19248 3653 5.1 %RANDOM
Rwork0.16231 ---
obs0.16384 68521 96.06 %-
all-75135 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.296 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.64→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4758 0 115 496 5369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225038
X-RAY DIFFRACTIONr_angle_refined_deg1.2622.0116848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5555638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91624200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.71315814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7391526
X-RAY DIFFRACTIONr_chiral_restr0.0850.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023810
X-RAY DIFFRACTIONr_nbd_refined0.2020.22491
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23534
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.2354
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.229
X-RAY DIFFRACTIONr_mcbond_it0.6841.53236
X-RAY DIFFRACTIONr_mcangle_it1.07925064
X-RAY DIFFRACTIONr_scbond_it1.91632098
X-RAY DIFFRACTIONr_scangle_it3.1284.51781
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 271 -
Rwork0.184 4937 -
obs--94.95 %

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