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- PDB-6l0k: Crystal structure of dihydroorotase in complex with malate at pH9... -

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Basic information

Entry
Database: PDB / ID: 6l0k
TitleCrystal structure of dihydroorotase in complex with malate at pH9 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 / cytosol / 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
(2S)-2-hydroxybutanedioic acid / Dihydroorotase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGuan, H.H. / Huang, Y.H. / Huang, C.Y. / Chen, C.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (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)166,97316
Polymers165,9134
Non-polymers1,06012
Water0
1
A: Dihydroorotase
C: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4878
Polymers82,9572
Non-polymers5306
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-20 kcal/mol
Surface area28020 Å2
MethodPISA
2
B: Dihydroorotase
D: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4878
Polymers82,9572
Non-polymers5306
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-19 kcal/mol
Surface area28140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.824, 88.856, 103.751
Angle α, β, γ (deg.)90.000, 95.380, 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 S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: URA4, YLR420W, L9931.1 / Production host: Escherichia coli (E. coli) / References: UniProt: P20051, dihydroorotase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid


Mass: 134.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 100mM MMT/sodium hydroxide pH 9, 26% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→46.156 Å / Num. obs: 22773 / % possible obs: 96.42 % / Redundancy: 3.7 % / CC1/2: 0.931 / Net I/σ(I): 17.7
Reflection shellResolution: 3.3→3.42 Å / Num. unique obs: 1822 / CC1/2: 0.74

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L0A

6l0a


Resolution: 3.3→46.156 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.29
RfactorNum. reflection% reflection
Rfree0.2656 1245 5.47 %
Rwork0.2138 --
obs0.2168 22759 96.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.79 Å2 / Biso mean: 41.3466 Å2 / Biso min: 10.21 Å2
Refinement stepCycle: final / Resolution: 3.3→46.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11368 0 44 0 11412
Biso mean--50.06 --
Num. residues----1455
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3-3.43180.3373970.2884196979
3.4318-3.58790.35031060.2524233794
3.5879-3.7770.31261240.2315239997
3.777-4.01350.30091350.22982459100
4.0135-4.32320.25711240.19832480100
4.3232-4.75790.26711550.2225245199
4.7579-5.44540.26471700.19382435100
5.4454-6.8570.25491490.21352503100
6.857-46.1560.2031850.1677248199

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