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- PDB-3w7l: Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in co... -

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Basic information

Entry
Database: PDB / ID: 3w7l
TitleStructure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-5-075
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-W7L / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 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 MII-5-075
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
Revision 1.3Nov 20, 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)71,63926
Polymers68,1342
Non-polymers3,50424
Water9,548530
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-31 kcal/mol
Surface area22220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.131, 71.785, 128.732
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) / 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, 554 molecules

#2: Chemical ChemComp-W7L / 5-[2-(6-methoxynaphthalen-1-yl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid


Mass: 340.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H16N2O5
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / 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.: 530 / 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: 2.31 Å3/Da / Density % sol: 46.76 % / Mosaicity: 0.839 °
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: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2009
RadiationMonochromator: SI(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 51501 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.107 / Χ2: 2.587 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.88-1.917.20.3879.3525712.09999.5
1.91-1.957.20.33825831.85799.8
1.95-1.987.20.2925541.89599.7
1.98-2.037.20.25825621.73799.4
2.03-2.077.20.22925702.00599.3
2.07-2.127.20.22125732.27100
2.12-2.177.20.1925682.00899.3
2.17-2.237.10.19125462.48799.2
2.23-2.297.20.16425692.20599.2
2.29-2.377.20.15925722.4499.1
2.37-2.457.10.15625722.97499
2.45-2.557.10.13425832.77299
2.55-2.6770.12425582.90298.8
2.67-2.816.90.11225983.18598.8
2.81-2.986.90.10225503.2197.8
2.98-3.216.90.08825803.35498.3
3.21-3.546.90.06525873.16697.7
3.54-4.056.80.05525613.17396.4
4.05-5.16.70.0525873.11596.1
5.1-506.60.05426573.12893.6

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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 3W7C

3w7c


Resolution: 1.88→31.76 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.257 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1886 2617 5.1 %RANDOM
Rwork0.1426 ---
obs0.1449 51326 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.14 Å2 / Biso mean: 16.2599 Å2 / Biso min: 5.1 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.88→31.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 233 530 5539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0195135
X-RAY DIFFRACTIONr_bond_other_d0.0030.024909
X-RAY DIFFRACTIONr_angle_refined_deg2.082.0296944
X-RAY DIFFRACTIONr_angle_other_deg1.0333.00211316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3385630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.95124.02204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98615814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8071527
X-RAY DIFFRACTIONr_chiral_restr0.1270.2767
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215685
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021114
LS refinement shellResolution: 1.878→1.926 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 208 -
Rwork0.143 3451 -
all-3659 -
obs--96.19 %

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