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- PDB-7wyf: Plasmodium falciparum dihydroorotate dehydrogenase (DHODH) in com... -

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Basic information

Entry
Database: PDB / ID: 7wyf
TitlePlasmodium falciparum dihydroorotate dehydrogenase (DHODH) in complex with its inhibitor 50
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrial
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / pfDHODH / Inhibitors / Complex / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase (quinone) activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane / nucleotide binding
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 ...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-7NE / 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: 3.3 Å
AuthorsZhu, L. / Li, H.
Funding support China, 1items
OrganizationGrant numberCountry
Other government81222046 China
CitationJournal: To Be Published
Title: Plasmodium falciparum dihydroorotate dehydrogenase (DHODH) in complex with its inhibitor 50
Authors: Zhu, L. / Li, H.
History
DepositionFeb 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
A: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8574
Polymers48,9471
Non-polymers9103
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-1 kcal/mol
Surface area15800 Å2
Unit cell
Length a, b, c (Å)57.710, 71.770, 179.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Dihydroorotate dehydrogenase (quinone), mitochondrial


Mass: 48946.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: dhod / Production host: Escherichia coli (E. coli)
References: UniProt: Q54A96, dihydroorotate dehydrogenase (quinone)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Chemical ChemComp-7NE / ethyl 2-(naphthalen-2-ylamino)-4-oxidanylidene-furan-3-carboxylate


Mass: 297.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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: 1.9 Å3/Da / Density % sol: 35.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M Tris-HCl (pH 7.5-9.5), 35 % (w/v) PEG 4000, 50 mM sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 3.3→54.94 Å / Num. obs: 5898 / % possible obs: 99.6 % / Redundancy: 5.9 % / CC1/2: 0.992 / Net I/σ(I): 9.6
Reflection shellResolution: 3.3→3.48 Å / Rmerge(I) obs: 0.537 / Num. unique obs: 848 / CC1/2: 0.892 / Rsym value: 0.587

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RX0

4rx0


Resolution: 3.3→45.99 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.781 / SU B: 57.295 / SU ML: 0.921 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.874 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3595 295 5 %RANDOM
Rwork0.2576 ---
obs0.2629 5602 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 166.97 Å2 / Biso mean: 69.311 Å2 / Biso min: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.55 Å2-0 Å20 Å2
2---4.41 Å2-0 Å2
3---7.96 Å2
Refinement stepCycle: final / Resolution: 3.3→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 64 2 2928
Biso mean--49.43 28.12 -
Num. residues----361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132977
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172813
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.6624011
X-RAY DIFFRACTIONr_angle_other_deg1.0881.5986550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5335358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.19424.326141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98715553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2841510
X-RAY DIFFRACTIONr_chiral_restr0.0520.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023254
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02586
LS refinement shellResolution: 3.3→3.386 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.518 25 -
Rwork0.368 411 -
all-436 -
obs--100 %

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