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- PDB-6l0h: Crystal structure of dihydroorotase in complex with malate at pH7... -

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Basic information

Entry
Database: PDB / ID: 6l0h
TitleCrystal structure of dihydroorotase in complex with malate at pH7 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: 2.054 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
Water18,7721042
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 area2210 Å2
ΔGint-18 kcal/mol
Surface area27600 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 area2250 Å2
ΔGint-20 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.569, 88.521, 103.293
Angle α, β, γ (deg.)90.000, 95.420, 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: ARG / End label comp-ID: ARG / Auth seq-ID: 2 - 364 / Label seq-ID: 2 - 364

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
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 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.: 1042 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100mM imidazole malate pH 7, 20% PEG 4000

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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: Apr 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→31.965 Å / Num. obs: 87644 / % possible obs: 91.55 % / Redundancy: 4.9 % / CC1/2: 0.908 / Net I/σ(I): 17.5
Reflection shellResolution: 2.05→2.13 Å / Num. unique obs: 3931 / CC1/2: 0.583

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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: 2.054→31.965 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.94
RfactorNum. reflection% reflection
Rfree0.2222 4396 5.02 %
Rwork0.1828 --
obs0.1848 87634 91.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.89 Å2 / Biso mean: 31.025 Å2 / Biso min: 8.63 Å2
Refinement stepCycle: final / Resolution: 2.054→31.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11344 0 44 1042 12430
Biso mean--24.59 34.52 -
Num. residues----1452
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4372X-RAY DIFFRACTION8.67TORSIONAL
12B4372X-RAY DIFFRACTION8.67TORSIONAL
13C4372X-RAY DIFFRACTION8.67TORSIONAL
14D4372X-RAY DIFFRACTION8.67TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0544-2.07780.3173470.24882928
2.0778-2.10220.3012660.2464129442
2.1022-2.12780.2747830.2433161254
2.1278-2.15480.29751170.242196765
2.1548-2.18310.2931210.2376238980
2.1831-2.2130.31711300.2312273790
2.213-2.24460.28541310.2339291296
2.2446-2.27810.29751480.2187296498
2.2781-2.31370.24251590.2247299899
2.3137-2.35160.29091500.21043016100
2.3516-2.39220.28121650.20613028100
2.3922-2.43560.25851340.20993009100
2.4356-2.48250.22631390.20773033100
2.4825-2.53310.24861550.20183050100
2.5331-2.58820.2661630.1963012100
2.5882-2.64840.26791430.20263010100
2.6484-2.71450.22991660.20063039100
2.7145-2.78790.23611580.19773011100
2.7879-2.86990.23841890.19662994100
2.8699-2.96250.23231470.20293054100
2.9625-3.06830.2441540.19883020100
3.0683-3.1910.23181830.18782981100
3.191-3.33610.24051910.19023003100
3.3361-3.51180.22741890.17472991100
3.5118-3.73150.18781950.1615298399
3.7315-4.01910.18221610.1557303799
4.0191-4.42260.16071710.149300499
4.4226-5.06040.17511550.1422303399
5.0604-6.36730.20251360.16813097100
6.3673-31.9650.18571500.14893131100

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