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- PDB-6l0j: Crystal structure of Dihydroorotase in complex with malate at pH7... -

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Basic information

Entry
Database: PDB / ID: 6l0j
TitleCrystal structure of Dihydroorotase in complex with malate at pH7.5 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
(2S)-2-hydroxybutanedioic acid / Dihydroorotase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.933 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: Molecules / Year: 2021
Title: Structural Analysis of Saccharomyces cerevisiae Dihydroorotase Reveals Molecular Insights into the Tetramerization Mechanism
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 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)166,97316
Polymers165,9134
Non-polymers1,06012
Water21,8341212
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 area2200 Å2
ΔGint-19 kcal/mol
Surface area27830 Å2
MethodPISA
2
D: Dihydroorotase
B: 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 area2280 Å2
ΔGint-20 kcal/mol
Surface area27700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.553, 88.337, 103.195
Angle α, β, γ (deg.)90.000, 95.600, 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


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.: 1212 / 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: 48.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM imidazole malate pH 7.5, 19% 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: 1.93→28.305 Å / Num. obs: 100526 / % possible obs: 99.9 % / Redundancy: 4.1 % / CC1/2: 0.875 / Net I/σ(I): 18.17
Reflection shellResolution: 1.93→2 Å / Num. unique obs: 2710 / CC1/2: 0.48

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L0A

6l0a


Resolution: 1.933→28.305 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.25
RfactorNum. reflection% reflection
Rfree0.229 4795 4.77 %
Rwork0.1826 --
obs0.1848 100526 87.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.55 Å2 / Biso mean: 24.9673 Å2 / Biso min: 4.72 Å2
Refinement stepCycle: final / Resolution: 1.933→28.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11360 0 44 1212 12616
Biso mean--18.79 30.38 -
Num. residues----1454
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9335-1.95540.2679250.284252114
1.9554-1.97840.3561460.264181223
1.9784-2.00260.3641520.2625125534
2.0026-2.02790.3054840.2513169347
2.0279-2.05460.28561180.2489225863
2.0546-2.08270.29781520.2312286680
2.0827-2.11250.27321770.2181323290
2.1125-2.1440.25361630.2154342495
2.144-2.17750.2641920.2139346997
2.1775-2.21320.25891940.2062357899
2.2132-2.25130.25072050.20413589100
2.2513-2.29220.24281810.20073595100
2.2922-2.33630.28691820.19963643100
2.3363-2.3840.261920.19073606100
2.384-2.43580.23531900.1893579100
2.4358-2.49240.26291790.19053599100
2.4924-2.55470.26261780.18573661100
2.5547-2.62370.27411560.18933649100
2.6237-2.70090.23741660.18763620100
2.7009-2.7880.23451630.18823642100
2.788-2.88750.221620.1873651100
2.8875-3.0030.23131540.19283625100
3.003-3.13950.24781660.18813658100
3.1395-3.30480.20981700.18743668100
3.3048-3.51150.23021760.17783619100
3.5115-3.78210.20152140.16023611100
3.7821-4.16160.21592200.1553586100
4.1616-4.76130.16721960.14733637100
4.7613-5.98940.18961590.16163686100
5.9894-28.3050.19581830.1631369999

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