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- PDB-7myd: Leishmania major dihydroorotate dehydrogenase in complex with 5-a... -

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Basic information

Entry
Database: PDB / ID: 7myd
TitleLeishmania major dihydroorotate dehydrogenase in complex with 5-amino-2-(1H-pyrrol-1-yl)benzonitrile
ComponentsDihydroorotate dehydrogenase (fumarate)
KeywordsOXIDOREDUCTASE / Leishmania major / neglected tropical disease / dihydroorotate dehydrogenase
Function / homology
Function and homology information


dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / fumarate metabolic process / dihydroorotate dehydrogenase activity / ciliary plasm / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / nucleotide binding / nucleoplasm / cytoplasm
Similarity search - Function
Dihydroorotate dehydrogenase, class 1A / Dihydroorotate dehydrogenase, class 1/ 2 / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / 5-azanyl-2-pyrrol-1-yl-benzenecarbonitrile / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPinheiro, M.P. / Cardoso, I.A. / Hunter, W.N. / Nonato, M.C.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2007/08703-0 Brazil
CitationJournal: To Be Published
Title: Leishmania major dihydroorotate dehydrogenase in complex with 5-amino-2-(1H-pyrrol-1-yl)benzonitrile
Authors: Pinheiro, M.P. / Cardoso, I.A. / Hunter, W.N. / Nonato, M.C.
History
DepositionMay 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Dihydroorotate dehydrogenase (fumarate)
BBB: Dihydroorotate dehydrogenase (fumarate)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,15211
Polymers76,4912
Non-polymers1,6609
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-72 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.071, 143.071, 68.997
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Dihydroorotate dehydrogenase (fumarate) / Dihydroorotate oxidase


Mass: 38245.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: DHODH, LMJF_16_0530 / Plasmid: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q4QEW7, dihydroorotate dehydrogenase (fumarate)

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Non-polymers , 5 types, 343 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SNQ / 5-azanyl-2-pyrrol-1-yl-benzenecarbonitrile


Mass: 183.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9N3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium citrate tribasic dihydrate, pH 5.6, 1.3 M lithium sulfate, 0.30 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.437 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.437 Å / Relative weight: 1
ReflectionResolution: 2.15→35.77 Å / Num. obs: 43015 / % possible obs: 97.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 11.9
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.803 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6253 / Rsym value: 0.803 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GYE

3gye


Resolution: 2.15→35.77 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.971 / SU ML: 0.124 / Cross valid method: FREE R-VALUE / ESU R: 0.197 / ESU R Free: 0.171
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2187 2164 5.031 %
Rwork0.1781 40847 -
all0.18 --
obs-43011 97.852 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.369 Å2
Baniso -1Baniso -2Baniso -3
1--0.055 Å2-0.028 Å2-0 Å2
2---0.055 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.15→35.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4612 0 109 334 5055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134905
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174595
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.6416660
X-RAY DIFFRACTIONr_angle_other_deg1.2731.5710564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3945624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.42322.603219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04215777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.641524
X-RAY DIFFRACTIONr_chiral_restr0.0610.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025636
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021132
X-RAY DIFFRACTIONr_nbd_refined0.1990.21100
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.24825
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22441
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.22293
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2387
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0870.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1740.214
X-RAY DIFFRACTIONr_nbd_other0.1530.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.214
X-RAY DIFFRACTIONr_mcbond_it1.4212.7292484
X-RAY DIFFRACTIONr_mcbond_other1.4152.7292483
X-RAY DIFFRACTIONr_mcangle_it2.2174.0883112
X-RAY DIFFRACTIONr_mcangle_other2.2184.0883113
X-RAY DIFFRACTIONr_scbond_it1.7242.8972421
X-RAY DIFFRACTIONr_scbond_other1.7232.8982422
X-RAY DIFFRACTIONr_scangle_it2.7634.2733548
X-RAY DIFFRACTIONr_scangle_other2.7624.2743549
X-RAY DIFFRACTIONr_lrange_it3.96432.6395743
X-RAY DIFFRACTIONr_lrange_other3.92832.5865721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.2060.311970.2562974X-RAY DIFFRACTION98.3866
2.206-2.2660.3071620.2662920X-RAY DIFFRACTION97.8723
2.266-2.3320.2291470.2172851X-RAY DIFFRACTION97.846
2.332-2.4040.2771070.2112826X-RAY DIFFRACTION98.7875
2.404-2.4830.2571480.2022694X-RAY DIFFRACTION97.9662
2.483-2.570.241430.1852574X-RAY DIFFRACTION97.5583
2.57-2.6670.2191380.1712471X-RAY DIFFRACTION97.3144
2.667-2.7750.1991420.1662382X-RAY DIFFRACTION97.3015
2.775-2.8990.2341230.1782315X-RAY DIFFRACTION97.559
2.899-3.040.2151090.1722213X-RAY DIFFRACTION97.0736
3.04-3.2040.221110.1772092X-RAY DIFFRACTION97.2198
3.204-3.3990.2131160.1741996X-RAY DIFFRACTION97.8231
3.399-3.6330.182900.1711889X-RAY DIFFRACTION97.4877
3.633-3.9240.192860.161758X-RAY DIFFRACTION98.874
3.924-4.2980.178840.1311653X-RAY DIFFRACTION98.6932
4.298-4.8050.159770.1331477X-RAY DIFFRACTION99.044
4.805-5.5470.203670.1631304X-RAY DIFFRACTION98.3501
5.547-6.790.238480.1831122X-RAY DIFFRACTION97.7444
6.79-9.5880.214460.169857X-RAY DIFFRACTION97.5162
9.588-35.770.248230.221480X-RAY DIFFRACTION94.3715

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