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- PDB-6l0g: Crystal structure of dihydroorotase in complex with malate at pH6... -

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Basic information

Entry
Database: PDB / ID: 6l0g
TitleCrystal structure of dihydroorotase in complex with malate at pH6 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 / nucleus / metal ion binding / 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: 2.053 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 / 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
B: Dihydroorotase
C: Dihydroorotase
D: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,97316
Polymers165,9134
Non-polymers1,06012
Water22,1401229
1
A: Dihydroorotase
C: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4878
Polymers82,9572
Non-polymers5306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-19 kcal/mol
Surface area27800 Å2
MethodPISA
2
B: Dihydroorotase
D: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4878
Polymers82,9572
Non-polymers5306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-20 kcal/mol
Surface area27940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.440, 88.544, 103.526
Angle α, β, γ (deg.)90.000, 95.390, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 2 through 364)
21chain B
31(chain C and resid 2 through 364)
41(chain D and resid 2 through 364)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 2 - 364 / Label seq-ID: 2 - 364

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 2 through 364)AA
2chain BBB
3(chain C and resid 2 through 364)CC
4(chain D and resid 2 through 364)DD

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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


Mass: 134.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1229 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 100mM imdazole malate pH 6, 17% PEG4000

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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: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→29.957 Å / Num. obs: 93410 / % possible obs: 97.25 % / Redundancy: 5.1 % / CC1/2: 0.943 / Net I/σ(I): 25.6
Reflection shellResolution: 2.05→2.13 Å / Num. unique obs: 7407 / CC1/2: 0.726

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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: 2.053→29.957 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.14
RfactorNum. reflection% reflection
Rfree0.2319 4699 5.03 %
Rwork0.1863 --
obs0.1887 93404 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.63 Å2 / Biso mean: 29.15 Å2 / Biso min: 8.59 Å2
Refinement stepCycle: final / Resolution: 2.053→29.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11368 0 44 1229 12641
Biso mean--25.29 33.83 -
Num. residues----1455
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4372X-RAY DIFFRACTION12.223TORSIONAL
12B4372X-RAY DIFFRACTION12.223TORSIONAL
13C4372X-RAY DIFFRACTION12.223TORSIONAL
14D4372X-RAY DIFFRACTION12.223TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.053-2.0760.32491150.2591192365
2.076-2.10040.26741400.2383241280
2.1004-2.1260.30661370.2193263587
2.126-2.15290.29761570.2263282893
2.1529-2.18130.30281570.2287292297
2.1813-2.21110.27381340.2213304699
2.2111-2.24270.25861400.21773045100
2.2427-2.27620.28571460.21753009100
2.2762-2.31170.26041640.21753043100
2.3117-2.34960.30021450.21573018100
2.3496-2.39010.25591650.20563035100
2.3901-2.43360.29191400.20813035100
2.4336-2.48040.27621390.20793049100
2.4804-2.5310.24551540.20183046100
2.531-2.5860.2941620.20063024100
2.586-2.64610.2681450.19113015100
2.6461-2.71220.21011680.19343047100
2.7122-2.78550.25071590.19933051100
2.7855-2.86740.27381880.19982996100
2.8674-2.95990.2311440.20253072100
2.9599-3.06560.23951610.20023043100
3.0656-3.18820.26341830.19592993100
3.1882-3.33310.26271900.19313026100
3.3331-3.50860.24631880.17913013100
3.5086-3.7280.1991960.16843009100
3.728-4.01520.18731630.16673059100
4.0152-4.41810.15721750.153301799
4.4181-5.05480.18131550.1477303799
5.0548-6.35850.20471380.17323111100
6.3585-29.9570.19881510.15553146100

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