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- PDB-8i3n: crystal structure of yeast cytosine deaminase mutant yCD-RQ -

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Basic information

Entry
Database: PDB / ID: 8i3n
Titlecrystal structure of yeast cytosine deaminase mutant yCD-RQ
ComponentsCytosine deaminase
KeywordsHYDROLASE / cytosine deaminase / mutant / 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsQin, M.M. / Yao, L.S. / Deng, H.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32201011 China
CitationJournal: To be published
Title: The crystal structure of rational designed yCD mutant yCD-RQ
Authors: Qin, M.M. / 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
C: Cytosine deaminase
D: Cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1938
Polymers79,9314
Non-polymers2624
Water9,800544
1
A: Cytosine deaminase
C: Cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0964
Polymers39,9662
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-91 kcal/mol
Surface area11950 Å2
MethodPISA
2
B: Cytosine deaminase
hetero molecules

D: Cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0964
Polymers39,9662
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area2510 Å2
ΔGint-92 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.669, 64.470, 83.092
Angle α, β, γ (deg.)90.00, 97.97, 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: 19982.752 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FCY1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12178, cytosine deaminase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.15M ammounium acetate, 27%-29% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97914 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.73→82.29 Å / Num. obs: 65362 / % possible obs: 96.9 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.043 / Rrim(I) all: 0.083 / Χ2: 0.86 / Net I/σ(I): 11.5
Reflection shellResolution: 1.73→1.82 Å / % possible obs: 97.8 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.48 / Num. measured all: 25357 / Num. unique obs: 9660 / CC1/2: 0.867 / Rpim(I) all: 0.35 / Rrim(I) all: 0.597 / Χ2: 0.61 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.10.1-2155refinement
XDSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→82.29 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2178 3615 3.04 %
Rwork0.2027 --
obs0.2032 65362 89.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→82.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4586 0 4 544 5134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064666
X-RAY DIFFRACTIONf_angle_d0.6096294
X-RAY DIFFRACTIONf_dihedral_angle_d24.1731694
X-RAY DIFFRACTIONf_chiral_restr0.064677
X-RAY DIFFRACTIONf_plane_restr0.003831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.750.34841260.3294222X-RAY DIFFRACTION84
1.75-1.770.32761320.30824160X-RAY DIFFRACTION85
1.77-1.80.3031290.30024207X-RAY DIFFRACTION84
1.8-1.830.24111300.28464197X-RAY DIFFRACTION85
1.83-1.850.29781500.27724708X-RAY DIFFRACTION94
1.85-1.880.31481490.26944683X-RAY DIFFRACTION95
1.88-1.910.28861260.2644025X-RAY DIFFRACTION87
1.92-1.950.27711140.26373497X-RAY DIFFRACTION91
1.95-1.990.2911540.24934795X-RAY DIFFRACTION95
1.99-2.030.29061480.23874635X-RAY DIFFRACTION95
2.03-2.070.2821500.23354705X-RAY DIFFRACTION94
2.07-2.120.23741370.22034666X-RAY DIFFRACTION94
2.12-2.180.22741480.21384666X-RAY DIFFRACTION94
2.18-2.230.28221510.21714633X-RAY DIFFRACTION93
2.23-2.30.24551420.21674571X-RAY DIFFRACTION93
2.3-2.370.25581460.2124576X-RAY DIFFRACTION92
2.37-2.460.21831400.21474549X-RAY DIFFRACTION92
2.46-2.560.20051440.20774546X-RAY DIFFRACTION92
2.56-2.670.21681420.19714542X-RAY DIFFRACTION91
2.67-2.810.19161390.19694424X-RAY DIFFRACTION90
2.82-2.990.18871360.20064345X-RAY DIFFRACTION88
2.99-3.220.19751350.19784394X-RAY DIFFRACTION88
3.22-3.550.22271350.17254424X-RAY DIFFRACTION89
3.55-4.060.16911420.15964417X-RAY DIFFRACTION89
4.06-5.110.17341360.1614319X-RAY DIFFRACTION87
5.12-82.290.18051340.18624303X-RAY DIFFRACTION87

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