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- PDB-6l0b: Crystal structure of dihydroorotase in complex with fluorouracil ... -

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Basic information

Entry
Database: PDB / ID: 6l0b
TitleCrystal structure of dihydroorotase in complex with fluorouracil 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-FLUOROURACIL / Dihydroorotase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)166,95716
Polymers165,9134
Non-polymers1,04412
Water4,071226
1
A: Dihydroorotase
C: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4798
Polymers82,9572
Non-polymers5226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-172 kcal/mol
Surface area27740 Å2
MethodPISA
2
B: Dihydroorotase
D: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4798
Polymers82,9572
Non-polymers5226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-174 kcal/mol
Surface area27950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.474, 88.430, 103.165
Angle α, β, γ (deg.)90.000, 95.410, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 2 - 365 / Label seq-ID: 2 - 365

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBC
3chain CCB
4chain DDD

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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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-URF / 5-FLUOROURACIL / Fluorouracil


Mass: 130.077 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H3FN2O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, chemotherapy*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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 / Details: 10 mM imidazole malate pH 7.0, 19 % 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: 2.7→29.94 Å / Num. obs: 41606 / % possible obs: 98.43 % / Redundancy: 4.1 % / CC1/2: 0.934 / Net I/σ(I): 9.9
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 3807 / CC1/2: 0.744

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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: 2.7→29.94 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 2009 4.83 %
Rwork0.1902 39597 -
obs0.193 41606 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.14 Å2 / Biso mean: 45.4831 Å2 / Biso min: 19.13 Å2
Refinement stepCycle: final / Resolution: 2.7→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11376 0 44 226 11646
Biso mean--43.8 37.42 -
Num. residues----1456
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4384X-RAY DIFFRACTION10.107TORSIONAL
12B4384X-RAY DIFFRACTION10.107TORSIONAL
13C4384X-RAY DIFFRACTION10.107TORSIONAL
14D4384X-RAY DIFFRACTION10.107TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.76720.32741270.2532258490
2.7672-2.8420.33761470.2429266194
2.842-2.92550.29161410.2397277297
2.9255-3.01990.2591370.2277282199
3.0199-3.12770.29511520.23312855100
3.1277-3.25280.28051340.22852862100
3.2528-3.40060.24971570.21362850100
3.4006-3.57970.28181100.19912895100
3.5797-3.80350.24411540.18392835100
3.8035-4.09650.23541680.18252876100
4.0965-4.50750.22281500.16622854100
4.5075-5.15690.20551160.15882920100
5.1569-6.48620.24361670.18362876100
6.4862-29.940.21931490.15282936100

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