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- PDB-8vll: Crystal structure of the yeast cytosine deaminase (yCD) M100W mutant -

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Basic information

Entry
Database: PDB / ID: 8vll
TitleCrystal structure of the yeast cytosine deaminase (yCD) M100W mutant
ComponentsCytosine deaminase
KeywordsANTIFUNGAL PROTEIN / cytosine deaminase / resistance / heterodimer
Function / homology
Function and homology information


cytidine metabolic process / pyrimidine-containing compound salvage / diaminohydroxyphosphoribosylaminopyrimidine deaminase activity / cytosine deaminase / cytosine deaminase activity / UMP salvage / cytosine metabolic process / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Cytidine and deoxycytidylate deaminase zinc-binding region / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like
Similarity search - Domain/homology
PHOSPHATE ION / Cytosine deaminase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsPicard, M.-E. / Grenier, J. / Despres, P.C. / Dube, A.K. / Landry, C.R. / Shi, R.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2020-06954 Canada
Fonds de Recherche du Quebec - Nature et Technologies (FRQNT)298169 Canada
CitationJournal: Science / Year: 2024
Title: Compensatory mutations potentiate constructive neutral evolution by gene duplication.
Authors: Despres, P.C. / Dube, A.K. / Picard, M.E. / Grenier, J. / Shi, R. / Landry, C.R.
History
DepositionJan 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 4, 2024Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Sep 18, 2024Group: Other / Category: pdbx_database_status
Item: _pdbx_database_status.process_site / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytosine deaminase
B: Cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,45713
Polymers35,7352
Non-polymers72211
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.839, 73.070, 92.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytosine deaminase / yCD / Cytosine aminohydrolase / Fluorocytosine resistance protein 1


Mass: 17867.309 Da / Num. of mol.: 2 / Mutation: M100W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FCY1, YPR062W, YP9499.17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12178, cytosine deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 8
Details: 0.2 M lithium chloride, 0.1 M Tris pH 8.0, 20% PEG-6000, cryoprotected by the reservoir solution supplemented with 15% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95299 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95299 Å / Relative weight: 1
ReflectionResolution: 1.67→46.41 Å / Num. obs: 35226 / % possible obs: 93.7 % / Redundancy: 4.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.048 / Rrim(I) all: 0.109 / Χ2: 0.75 / Net I/σ(I): 9.3 / Num. measured all: 168835
Reflection shellResolution: 1.67→1.7 Å / % possible obs: 62.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.492 / Num. measured all: 3782 / Num. unique obs: 1151 / CC1/2: 0.729 / Rpim(I) all: 0.308 / Rrim(I) all: 0.583 / Χ2: 0.27 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimlessdata scaling
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→41.85 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.731 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17907 1762 5 %RANDOM
Rwork0.15772 ---
obs0.15881 33420 93.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.685 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-0 Å2
2--0.17 Å20 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.67→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 39 214 2616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132459
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172269
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.6543294
X-RAY DIFFRACTIONr_angle_other_deg1.5581.595282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6195306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43823.125128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22615444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8141514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022748
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02502
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7331.6581215
X-RAY DIFFRACTIONr_mcbond_other1.7331.6541213
X-RAY DIFFRACTIONr_mcangle_it2.432.4741518
X-RAY DIFFRACTIONr_mcangle_other2.432.4741518
X-RAY DIFFRACTIONr_scbond_it3.3032.121244
X-RAY DIFFRACTIONr_scbond_other3.3022.1211245
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7862.9871775
X-RAY DIFFRACTIONr_long_range_B_refined5.76321.0632891
X-RAY DIFFRACTIONr_long_range_B_other5.65720.7642849
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 63 -
Rwork0.224 1639 -
obs--62.3 %

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