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- PDB-8vlj: Crystal structure of the cacodylate-bound yeast cytosine deaminas... -

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Basic information

Entry
Database: PDB / ID: 8vlj
TitleCrystal structure of the cacodylate-bound yeast cytosine deaminase (closed form)
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
CACODYLATE ION / Cytosine deaminase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 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

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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)36,1779
Polymers35,6252
Non-polymers5527
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-84 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.108, 55.073, 66.867
Angle α, β, γ (deg.)90.00, 90.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 17812.297 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 319 molecules

#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.02 Å3/Da / Density % sol: 39.15 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6
Details: 0.1 M sodium cacodylate pH 6.0, 15% PEG-4000, 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: APS / Beamline: 31-ID / Wavelength: 1.04339 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04339 Å / Relative weight: 1
ReflectionResolution: 1.39→66.86 Å / Num. obs: 54840 / % possible obs: 96 % / Redundancy: 4.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.073 / Rrim(I) all: 0.164 / Net I/σ(I): 7.9 / Num. measured all: 248657
Reflection shellResolution: 1.39→1.47 Å / % possible obs: 80.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.723 / Num. measured all: 24434 / Num. unique obs: 6692 / CC1/2: 0.534 / Rpim(I) all: 0.465 / Rrim(I) all: 0.935 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→42.55 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.869 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16688 2698 4.9 %RANDOM
Rwork0.14187 ---
obs0.14312 52083 95.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.941 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0 Å20.05 Å2
2--0.28 Å2-0 Å2
3----0.61 Å2
Refinement stepCycle: 1 / Resolution: 1.39→42.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 21 312 2719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132523
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182359
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.6553398
X-RAY DIFFRACTIONr_angle_other_deg1.6081.5975511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42622.932133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11815480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.541516
X-RAY DIFFRACTIONr_chiral_restr0.1050.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022865
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02515
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_it0.9260.8011256
X-RAY DIFFRACTIONr_mcbond_other0.9260.8011255
X-RAY DIFFRACTIONr_mcangle_it1.4261.1991575
X-RAY DIFFRACTIONr_mcangle_other1.4261.21576
X-RAY DIFFRACTIONr_scbond_it2.1951.071267
X-RAY DIFFRACTIONr_scbond_other2.1941.071268
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2681.4991814
X-RAY DIFFRACTIONr_long_range_B_refined4.30610.9673021
X-RAY DIFFRACTIONr_long_range_B_other4.0310.3782947
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.39→1.426 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 127 -
Rwork0.225 2974 -
obs--73.87 %

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