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- PDB-7t6h: E. coli dihydroorotate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 7t6h
TitleE. coli dihydroorotate dehydrogenase
ComponentsDihydroorotate dehydrogenase (quinone)Dihydroorotate dehydrogenase (quinone)
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


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 / FMN binding / membrane / plasma membrane / cytosol
Similarity search - Function
Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone)
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.42 Å
AuthorsHorwitz, S.M. / Ambarian, J.A. / Davis, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Rsc Chem Biol / Year: 2022
Title: Structural insights into inhibition of the drug target dihydroorotate dehydrogenase by bacterial hydroxyalkylquinolines.
Authors: Horwitz, S.M. / Blue, T.C. / Ambarian, J.A. / Hoshino, S. / Seyedsayamdost, M.R. / Davis, K.M.
History
DepositionDec 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase (quinone)
B: Dihydroorotate dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7956
Polymers80,5712
Non-polymers1,2254
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-7 kcal/mol
Surface area25430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.525, 169.495, 129.984
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Dihydroorotate dehydrogenase (quinone) / Dihydroorotate dehydrogenase (quinone) / DHOdehase / DHOD / DHODase / Dihydroorotate oxidase


Mass: 40285.258 Da / Num. of mol.: 2 / Mutation: 0
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: pyrD, b0945, JW0928 / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A7E1, dihydroorotate dehydrogenase (quinone)
#2: Chemical ChemComp-ORO / OROTIC ACID / Orotic acid


Mass: 156.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 3.92 Å3/Da / Density % sol: 68.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: sodium malonate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03384 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2021
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03384 Å / Relative weight: 1
ReflectionResolution: 2.42→49.7 Å / Num. obs: 43993 / % possible obs: 99.23 % / Redundancy: 7.6 % / Biso Wilson estimate: 57.15 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.1582 / Rpim(I) all: 0.06132 / Rrim(I) all: 0.17 / Net I/σ(I): 8.06
Reflection shellResolution: 2.42→2.506 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.633 / Num. unique obs: 4336 / CC1/2: 0.5 / CC star: 0.817 / Rpim(I) all: 0.6226 / % possible all: 99.18

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SIR / Resolution: 2.42→49.7 Å / SU ML: 0.3789 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.6986
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2354 1617 3.67 %
Rwork0.2004 42476 -
obs0.2017 43993 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.19 Å2
Refinement stepCycle: LAST / Resolution: 2.42→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5125 0 84 134 5343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00925297
X-RAY DIFFRACTIONf_angle_d1.13637181
X-RAY DIFFRACTIONf_chiral_restr0.0659816
X-RAY DIFFRACTIONf_plane_restr0.0076934
X-RAY DIFFRACTIONf_dihedral_angle_d17.20561991
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.490.38791360.35173449X-RAY DIFFRACTION97.15
2.49-2.570.34551370.28693483X-RAY DIFFRACTION99.29
2.57-2.660.2941320.25953475X-RAY DIFFRACTION99.28
2.66-2.770.28291200.24433578X-RAY DIFFRACTION99.46
2.77-2.890.27371370.24443432X-RAY DIFFRACTION97.81
2.89-3.040.30571330.2653533X-RAY DIFFRACTION99.62
3.04-3.240.3181380.24133544X-RAY DIFFRACTION99.78
3.24-3.480.27851360.21253554X-RAY DIFFRACTION99.68
3.49-3.840.23111300.20623567X-RAY DIFFRACTION99.7
3.84-4.390.18211340.17173540X-RAY DIFFRACTION98.45
4.39-5.530.20831390.15763619X-RAY DIFFRACTION99.84
5.53-49.70.18631450.16753702X-RAY DIFFRACTION98.84

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