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- PDB-4ef9: Crystal structure of dihydroorotate dehydrogenase from Leishmania... -

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Basic information

Entry
Database: PDB / ID: 4ef9
TitleCrystal structure of dihydroorotate dehydrogenase from Leishmania major in complex with 4-Nitrophenyl isothiocyanate
ComponentsDihydroorotate dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Leishmania major / dihydroorotate dehydrogenase / 4-Nitrophenyl isothiocyanate / pyrd / Oxidoreductase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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 ...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
N-(4-nitrophenyl)thioformamide / FLAVIN MONONUCLEOTIDE / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPinheiro, M.P. / Emery, F.S. / Nonato, M.C.
CitationJournal: Curr.Pharm.Des. / Year: 2013
Title: Target sites for the design of anti-trypanosomatid drugs based on the structure of dihydroorotate dehydrogenase.
Authors: Pinheiro, M.P. / Emery, F.S. / Nonato, M.C.
History
DepositionMar 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Sep 13, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)78,45315
Polymers76,3192
Non-polymers2,13413
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-158 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.910, 143.910, 69.621
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: 38159.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: DHODH, lmjf16.0530, LMJF_16_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, 549 molecules

#2: Chemical ChemComp-4NF / N-(4-nitrophenyl)thioformamide / 4-NITROPHENYL ISOTHIOCYANATE, bound form


Mass: 182.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6N2O2S
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer details4-NITROPHENYL ISOTHIOCYANATE REACTS WITH THE CYS 150 OF DIHYDROOROTATE DEHYDROGENASE. THE FINAL ...4-NITROPHENYL ISOTHIOCYANATE REACTS WITH THE CYS 150 OF DIHYDROOROTATE DEHYDROGENASE. THE FINAL REACTION PRODUCT IS COMPONENT 4NF.

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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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M SODIUM CITRATE TRIBASIC DIHYDRATE pH 5.6, 1.3M LITHIUM SULFATE, 0.3M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.305 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2011
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.305 Å / Relative weight: 1
ReflectionResolution: 1.6→23.47 Å / Num. all: 108237 / Num. obs: 108237 / % possible obs: 100 % / Observed criterion σ(I): 2.5 / Redundancy: 11.7 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 17.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 11 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 4.1 / Num. unique all: 15723 / Rsym value: 0.77 / % possible all: 100

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Processing

Software
NameVersionClassification
NatXraysoftwaredata collection
MOLREPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GYE

3gye


Resolution: 1.6→22.68 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1849 5401 5 %RANDOM
Rwork0.16767 ---
obs0.16855 102786 99.94 %-
all-102786 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.285 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→22.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 133 536 5367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.025005
X-RAY DIFFRACTIONr_angle_refined_deg1.2672.0026807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1185636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.86324.293198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.86615780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3271523
X-RAY DIFFRACTIONr_chiral_restr0.0760.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213787
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 382 -
Rwork0.241 7532 -
obs--100 %

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