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- PDB-1uum: Rat dihydroorotate dehydrogenase (DHOD)in complex with atovaquone -

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Basic information

Entry
Database: PDB / ID: 1uum
TitleRat dihydroorotate dehydrogenase (DHOD)in complex with atovaquone
ComponentsDIHYDROOROTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DIHYDROOROTATE DEHYDROGENASE / BREQUINAR / ATOVAQUONE / NUCLEOTIDE METABOLISM / PYRIMIDINE BIOSYNTHESIS / FAD / FLAVOPROTEIN / TRANSIT PEPTIDE
Function / homology
Function and homology information


Pyrimidine biosynthesis / response to L-arginine / pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase activity / dihydroorotase activity / UDP biosynthetic process / response to caffeine / response to starvation ...Pyrimidine biosynthesis / response to L-arginine / pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase activity / dihydroorotase activity / UDP biosynthetic process / response to caffeine / response to starvation / regulation of mitochondrial fission / ubiquinone binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / quinone binding / lactation / female pregnancy / : / FMN binding / mitochondrial inner membrane / positive regulation of apoptotic process / response to xenobiotic stimulus / neuronal cell body
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-AFI / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesRATTUS RATTUS (black rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHansen, M. / Le Nours, J. / Johansson, E. / Antal, T. / Ullrich, A. / Loffler, M. / Larsen, S.
CitationJournal: Protein Sci. / Year: 2004
Title: Inhibitor Binding in a Class 2 Dihydroorotate Dehydrogenase Causes Variations in the Membrane-Associated N-Terminal Domain
Authors: Hansen, M. / Le Nours, J. / Johansson, E. / Antal, T. / Ullrich, A. / Loffler, M. / Larsen, S.
History
DepositionJan 6, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: diffrn_source / exptl_crystal_grow
Item: _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.method
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROOROTATE DEHYDROGENASE
B: DIHYDROOROTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,22510
Polymers80,6822
Non-polymers2,5438
Water3,693205
1
A: DIHYDROOROTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6135
Polymers40,3411
Non-polymers1,2724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: DIHYDROOROTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6135
Polymers40,3411
Non-polymers1,2724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)133.150, 133.150, 50.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (0.5, 0.866), (-0.866, 0.5), (1) / Vector: -66.57247, 115.32687, 75.21201)

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein DIHYDROOROTATE DEHYDROGENASE / MITOCHONDRIAL PRECURSOR / DIHYDROOROTATE OXIDASE / DHODEHASE


Mass: 40340.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS RATTUS (black rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q63707, EC: 1.3.99.11
#5: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 211 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Chemical ChemComp-AFI / 2-[4-(4-CHLOROPHENYL)CYCLOHEXYLIDENE]-3,4-DIHYDROXY-1(2H)-NAPHTHALENONE


Mass: 366.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H19ClO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYTIC ACTIVITY: (S)-DIHYDROOROTATE + O2 = OROTATE + H2O2
Sequence details29 FIRST RESIDUES IN N-TERMINAL DELETED AND HIS-TAQ ADDED

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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 Å3/Da / Density % sol: 59 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: VAPOUR DIFFUSION HANGING DROP WITH MOTHER LIQUOR, 5% PEG400, 1.9 M AMMONIUM SULPHATE, 0.1 M TRIS-HCL PH 8.6, PROTEIN SOLUTION: 15 MG/ML PROTEIN, 2 MM OROTATE, 0.1 % BETA-OCTYLGLUCOSIDE, 0.1 MM ATOVAQUONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9999
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 44018 / % possible obs: 99.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.055
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.306 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2183 5 %RANDOM
Rwork0.216 ---
obs0.216 43995 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.1905 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å22.35 Å20 Å2
2---0.22 Å20 Å2
3---0.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5316 0 176 205 5697
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 332 4.6 %
Rwork0.255 6937 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMLIGAND_NEW.TOP
X-RAY DIFFRACTION3LIGAND_NEW.PAR
X-RAY DIFFRACTION4WATER.PARAM

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