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- PDB-5tce: N-terminal microdomain of 34-mers from HsDHODH - N-t(DH) -

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Basic information

Entry
Database: PDB / ID: 5tce
TitleN-terminal microdomain of 34-mers from HsDHODH - N-t(DH)
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrialDihydroorotate dehydrogenase (quinone)
KeywordsOXIDOREDUCTASE / micelles
Function / homology
Function and homology information


pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane ...pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane / mitochondrion / nucleoplasm / cytosol
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-type TIM barrel
Similarity search - Domain/homology
Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsCrusca, E. / Munte, C.E.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)10/12953-4 Brazil
CitationJournal: J Phys Chem B / Year: 2015
Title: Conformational changes of the HsDHODH N-terminal Microdomain via DEER Spectroscopy.
Authors: Vicente, E.F. / Sahu, I.D. / Costa-Filho, A.J. / Cilli, E.M. / Lorigan, G.A.
History
DepositionSep 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Refinement description
Category: pdbx_audit_support / pdbx_nmr_refine / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase (quinone), mitochondrial


Theoretical massNumber of molelcules
Total (without water)3,8311
Polymers3,8311
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area120 Å2
ΔGint1 kcal/mol
Surface area3160 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Dihydroorotate dehydrogenase (quinone), mitochondrial / Dihydroorotate dehydrogenase (quinone) / DHOdehase / Dihydroorotate oxidase


Mass: 3831.320 Da / Num. of mol.: 1 / Fragment: residues 32-65 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D DQF-COSY
131isotropic12D 1H-1H NOESY
141isotropic22D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 700 uM peptide, 90% H2O/10% D2O / Details: TRIS 10 mM DPC-d38 100 mM / Label: DH-34 - DPC micelle / Solvent system: 90% H2O/10% D2O
SampleConc.: 700 uM / Component: peptide / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 7.4 / Pressure: ambient atm / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificchemical shift calculation
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 8
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 20

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