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- PDB-8vlk: Crystal structure of the yeast cytosine deaminase containing both... -

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Basic information

Entry
Database: PDB / ID: 8vlk
TitleCrystal structure of the yeast cytosine deaminase containing both open and closed active sites
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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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
C: Cytosine deaminase
D: Cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,07516
Polymers71,2494
Non-polymers82612
Water7,404411
1
A: Cytosine deaminase
B: Cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1009
Polymers35,6252
Non-polymers4757
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-87 kcal/mol
Surface area12600 Å2
MethodPISA
2
C: Cytosine deaminase
D: Cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9767
Polymers35,6252
Non-polymers3515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-102 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.865, 40.825, 97.728
Angle α, β, γ (deg.)90.00, 104.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17812.297 Da / Num. of mol.: 4
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6
Details: 0.2 M lithium sulfate, 0.1 M MES pH 6.0 and 20% 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: 1.27899 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27899 Å / Relative weight: 1
ReflectionResolution: 1.76→94.49 Å / Num. obs: 58759 / % possible obs: 98.8 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.038 / Rrim(I) all: 0.099 / Net I/σ(I): 12.2 / Num. measured all: 387827
Reflection shellResolution: 1.76→1.86 Å / % possible obs: 99.1 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.883 / Num. measured all: 55282 / Num. unique obs: 8542 / CC1/2: 0.736 / Rpim(I) all: 0.41 / Rrim(I) all: 1.055 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→52.74 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.748 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2895 4.9 %RANDOM
Rwork0.16148 ---
obs0.16308 55849 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.805 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å2-1.12 Å2
2--0.1 Å20 Å2
3---0.96 Å2
Refinement stepCycle: 1 / Resolution: 1.76→52.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4745 0 38 411 5194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134883
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174540
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.6496547
X-RAY DIFFRACTIONr_angle_other_deg1.4671.5910575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2595615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76522.813256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32315906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1041531
X-RAY DIFFRACTIONr_chiral_restr0.0850.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025487
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02998
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_it2.1782.552448
X-RAY DIFFRACTIONr_mcbond_other2.1752.5472446
X-RAY DIFFRACTIONr_mcangle_it2.9433.813055
X-RAY DIFFRACTIONr_mcangle_other2.9443.813055
X-RAY DIFFRACTIONr_scbond_it3.4683.0112435
X-RAY DIFFRACTIONr_scbond_other3.4523.0032428
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1794.3183477
X-RAY DIFFRACTIONr_long_range_B_refined6.29431.2685738
X-RAY DIFFRACTIONr_long_range_B_other6.25831.0165666
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 211 -
Rwork0.275 4075 -
obs--99.01 %

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