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- PDB-6l0f: Crystal structure of dihydroorotase in complex with 5-Aminouracil... -

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Basic information

Entry
Database: PDB / ID: 6l0f
TitleCrystal structure of dihydroorotase in complex with 5-Aminouracil from Saccharomyces cerevisiae
ComponentsDihydroorotase
KeywordsHYDROLASE / Dihydropyrimidinase Dihydroorotase metalloenzyme
Function / homology
Function and homology information


dihydroorotase / pyrimidine nucleotide biosynthetic process / dihydroorotase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Dihydroorotase homodimeric type / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
5-AMINO-1H-PYRIMIDINE-2,4-DIONE / Dihydroorotase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.26 Å
AuthorsGuan, H.H. / Huang, Y.H. / Huang, C.Y. / Chen, C.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural basis for the interaction modes of dihydroorotase with the anticancer drugs 5-fluorouracil and 5-aminouracil.
Authors: Guan, H.H. / Huang, Y.H. / Lin, E.S. / Chen, C.J. / Huang, C.Y.
History
DepositionSep 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotase
B: Dihydroorotase
C: Dihydroorotase
D: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,94516
Polymers165,9134
Non-polymers1,03212
Water905
1
A: Dihydroorotase
B: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4738
Polymers82,9572
Non-polymers5166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-173 kcal/mol
Surface area27710 Å2
MethodPISA
2
C: Dihydroorotase
D: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4738
Polymers82,9572
Non-polymers5166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-172 kcal/mol
Surface area27940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.649, 88.739, 103.395
Angle α, β, γ (deg.)90.000, 95.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dihydroorotase / DHOase


Mass: 41478.355 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P20051, dihydroorotase
#2: Chemical
ChemComp-WBU / 5-AMINO-1H-PYRIMIDINE-2,4-DIONE


Mass: 127.101 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H5N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 10 mM imidazole malate pH 7.1, 18 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Jun 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.26→34.3 Å / Num. obs: 24080 / % possible obs: 99.13 % / Redundancy: 4 % / CC1/2: 0.926 / Net I/σ(I): 8.6
Reflection shellResolution: 3.26→3.37 Å / Num. unique obs: 2299 / CC1/2: 0.686

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L0A

6l0a


Resolution: 3.26→34.3 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 1160 4.82 %
Rwork0.1998 22920 -
obs0.2027 24080 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118 Å2 / Biso mean: 61.8527 Å2 / Biso min: 28.04 Å2
Refinement stepCycle: final / Resolution: 3.26→34.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11376 0 44 5 11425
Biso mean--69.6 40.75 -
Num. residues----1456
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.26-3.410.32151360.26882784292097
3.41-3.590.3351630.24692826298999
3.59-3.810.27741210.227228823003100
3.81-4.110.2931360.205328973033100
4.11-4.520.25421520.185828573009100
4.52-5.170.21821380.172828943032100
5.17-6.510.28591510.201628903041100
6.51-34.30.20451630.17312890305398

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