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- PDB-3mhu: Crystal structure of dihydroorotate dehydrogenase from Leishmania... -

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Basic information

Entry
Database: PDB / ID: 3mhu
TitleCrystal structure of dihydroorotate dehydrogenase from Leishmania major in complex with 5-Nitroorotic acid
ComponentsDihydroorotate dehydrogenase
KeywordsOXIDOREDUCTASE / dihydroorotate dehydrogenase / pyrd
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 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-EJZ / FLAVIN MONONUCLEOTIDE / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPinheiro, M.P. / Rocha, J.R. / Cheleski, J. / Montanari, C.A. / Nonato, M.C.
CitationJournal: Eur.J.Med.Chem. / Year: 2010
Title: Novel insights for dihydroorotate dehydrogenase class 1A inhibitors discovery.
Authors: Cheleski, J. / Rocha, J.R. / Pinheiro, M.P. / Wiggers, H.J. / da Silva, A.B. / Nonato, M.C. / Montanari, C.A.
History
DepositionApr 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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

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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)76,55312
Polymers74,6812
Non-polymers1,87110
Water10,449580
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-51 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.562, 141.562, 68.811
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dihydroorotate dehydrogenase /


Mass: 37340.723 Da / Num. of mol.: 2 / Fragment: UNP residues 1-312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: LmjF16.0530 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q4QEW7, EC: 1.3.3.1

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Non-polymers , 5 types, 590 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-EJZ / 5-nitro-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid / 5 Nitroorotic Acid


Mass: 201.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H3N3O6
#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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M sodium citrate tribasic dihydrate pH 5.6, 1.1M lithium sulfate, 0.45M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.437 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 1, 2009
RadiationMonochromator: Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.437 Å / Relative weight: 1
ReflectionResolution: 1.85→31.47 Å / Num. obs: 65142 / % possible obs: 97.6 % / Observed criterion σ(I): 2.5 / Redundancy: 6.3 % / Biso Wilson estimate: 20.54 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 14.9
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 6 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 2.7 / Num. unique all: 9593 / Rsym value: 0.552 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GYE

3gye


Resolution: 1.85→31.47 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.281 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19397 3295 5.1 %RANDOM
Rwork0.15815 ---
obs0.15995 61820 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.691 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→31.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4645 0 125 580 5350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225018
X-RAY DIFFRACTIONr_angle_refined_deg1.24826828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.21524.286210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30315820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8451527
X-RAY DIFFRACTIONr_chiral_restr0.0870.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213829
X-RAY DIFFRACTIONr_mcbond_it1.5421.53123
X-RAY DIFFRACTIONr_mcangle_it2.39125023
X-RAY DIFFRACTIONr_scbond_it4.03331895
X-RAY DIFFRACTIONr_scangle_it5.764.51786
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 216 -
Rwork0.274 4661 -
obs--98.57 %

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