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- PDB-8i3p: crystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SA... -

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Basic information

Entry
Database: PDB / ID: 8i3p
Titlecrystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SAH in complex with (R)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one
ComponentsCytosine deaminase
KeywordsHYDROLASE / metalloenzyme
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
4-oxidanyl-3,4-dihydro-1H-pyrimidin-2-one / Cytosine deaminase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsQin, M.M. / Deng, H.Z. / Yao, L.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32201011 China
CitationJournal: To be published
Title: crystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SAH in complex with (R)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one
Authors: Qin, M.M. / Deng, H.Z. / Yao, L.S.
History
DepositionJan 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,0138
Polymers45,5302
Non-polymers4836
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-18 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.175, 68.900, 49.424
Angle α, β, γ (deg.)90.00, 101.58, 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: 22764.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: FCY1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12178, cytosine deaminase
#2: Chemical ChemComp-OS0 / 4-oxidanyl-3,4-dihydro-1H-pyrimidin-2-one


Mass: 114.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 1.96 Å3/Da / Density % sol: 31.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.5 M Ammonium sulfate, 0.1 M Tris pH 8.5, 12% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.18→48.42 Å / Num. obs: 69899 / % possible obs: 85.6 % / Redundancy: 2.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.031 / Rrim(I) all: 0.053 / Χ2: 0.46 / Net I/σ(I): 9.5 / Num. measured all: 223856
Reflection shellResolution: 1.18→1.24 Å / % possible obs: 81.1 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.262 / Num. measured all: 27029 / Num. unique obs: 12501 / CC1/2: 0.902 / Rpim(I) all: 0.22 / Rrim(I) all: 0.344 / Χ2: 0.39 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
Aimless0.7.4data scaling
XDSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→33.41 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1614 1511 2.22 %
Rwork0.1413 --
obs0.1417 68147 85.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→33.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 26 349 2877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162574
X-RAY DIFFRACTIONf_angle_d1.4473458
X-RAY DIFFRACTIONf_dihedral_angle_d15.422956
X-RAY DIFFRACTIONf_chiral_restr0.116370
X-RAY DIFFRACTIONf_plane_restr0.011454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.340.20081380.1646241X-RAY DIFFRACTION89
1.34-1.390.15691410.14666241X-RAY DIFFRACTION89
1.39-1.450.16441430.13656277X-RAY DIFFRACTION89
1.45-1.510.17071420.12756244X-RAY DIFFRACTION89
1.51-1.590.14781340.12326146X-RAY DIFFRACTION87
1.59-1.690.16731380.12326138X-RAY DIFFRACTION87
1.69-1.820.15271440.13086101X-RAY DIFFRACTION87
1.82-20.15941370.13735991X-RAY DIFFRACTION85
2-2.290.16261370.13615977X-RAY DIFFRACTION85
2.29-2.890.17541410.1495769X-RAY DIFFRACTION82
2.89-33.410.14811160.15155511X-RAY DIFFRACTION77

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