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- PDB-1tv5: Plasmodium falciparum dihydroorotate dehydrogenase with a bound i... -

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Basic information

Entry
Database: PDB / ID: 1tv5
TitlePlasmodium falciparum dihydroorotate dehydrogenase with a bound inhibitor
ComponentsDihydroorotate dehydrogenase homolog, mitochondrial
KeywordsOXIDOREDUCTASE / alpha-beta barrel / tim barrel
Function / homology
Function and homology information


Pyrimidine biosynthesis / pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane
Similarity search - Function
Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-A26 / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHurt, D.E. / Widom, J. / Clardy, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of Plasmodium falciparum dihydroorotate dehydrogenase with a bound inhibitor.
Authors: Hurt, D.E. / Widom, J. / Clardy, J.
History
DepositionJun 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 18, 2012Group: Non-polymer description
Revision 1.4Aug 23, 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

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9407
Polymers50,2601
Non-polymers1,6806
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dihydroorotate dehydrogenase homolog, mitochondrial
hetero molecules

A: Dihydroorotate dehydrogenase homolog, mitochondrial
hetero molecules

A: Dihydroorotate dehydrogenase homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,82021
Polymers150,7813
Non-polymers5,03918
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area14520 Å2
ΔGint-136 kcal/mol
Surface area41300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.428, 105.428, 276.632
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Cell settingtrigonal
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1006-

SO4

21A-1006-

SO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dihydroorotate dehydrogenase homolog, mitochondrial / E.C.1.3.3.1,E.C.1.3.99.11 / Dihydroorotate oxidase / DHOdehase / dihydroorotate dehydrogenase


Mass: 50260.262 Da / Num. of mol.: 1 / Fragment: Fully functional N-terminal deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: dhod / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q08210, EC: 1.3.99.11, EC: 1.3.3.1

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Non-polymers , 6 types, 218 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A26 / (2Z)-2-cyano-3-hydroxy-N-[4-(trifluoromethyl)phenyl]but-2-enamide / ANTIPROLIFERATIVE AGENT A771726 / Teriflunomide


Mass: 270.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9F3N2O2 / Comment: medication*YM
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical ChemComp-ORO / OROTIC ACID / Orotic acid


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#6: Chemical ChemComp-N8E / 3,6,9,12,15-PENTAOXATRICOSAN-1-OL / N-OCTYLPENTAOXYETHYLENE / PENTAETHYLENE GLYCOL MONOOCTYL ETHER / OCTYLPENTAGLYCOL N-OCTYLPENTAOXYETHYLENE


Mass: 350.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O6 / Comment: C8E5, detergent*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.3
Details: ammonium sulfate, sodium acetate, C8E5, dihydroorotic acid, A77 1726, pH 4.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9474 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 10, 2002
RadiationMonochromator: Horizontal focussing, 5.05 deg asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9474 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 23068 / Num. obs: 23068 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 32.6 Å2 / Rsym value: 0.074 / Net I/σ(I): 8.6
Reflection shellResolution: 2.4→2.52 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3376 / % possible all: 99.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
RESOLVEmodel building
CNS1refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homo sapiens DHODH, PDB ID: 1D3H

1d3h


Resolution: 2.4→33.48 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2853804.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Sulfate ion was in a special position and could not be refined
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1139 5 %RANDOM
Rwork0.201 ---
all0.208 22925 --
obs0.2011 21786 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.9279 Å2 / ksol: 0.400789 e/Å3
Displacement parametersBiso mean: 35.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.78 Å22.74 Å20 Å2
2--3.78 Å20 Å2
3----7.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.4→33.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 114 212 3270
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scbond_it2.242
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 186 4.9 %
Rwork0.22 3649 -
obs-3810 98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2LIGS.PARAMLIGS.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP

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