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- PDB-8i3o: crystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SAH -

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Basic information

Entry
Database: PDB / ID: 8i3o
Titlecrystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SAH
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
: / Cytosine deaminase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: crystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SAH
Authors: Qin, M.M. / Yao, L.S. / Deng, H.Z.
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

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)84,0438
Polymers83,8234
Non-polymers2204
Water9,170509
1
A: Cytosine deaminase
hetero molecules

C: Cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0214
Polymers41,9112
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area2530 Å2
ΔGint-27 kcal/mol
Surface area11960 Å2
MethodPISA
2
B: Cytosine deaminase
D: Cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0214
Polymers41,9112
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-26 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.319, 64.273, 83.092
Angle α, β, γ (deg.)90.00, 97.69, 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: 20955.725 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 1.94 Å3/Da / Density % sol: 36.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.15M ammounium acetate, 25%-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 EIGER2 S 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: 1.64→60.77 Å / Num. obs: 41979 / % possible obs: 97.1 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.042 / Rrim(I) all: 0.105 / Χ2: 0.89 / Net I/σ(I): 10 / Num. measured all: 479992
Reflection shellResolution: 1.64→1.73 Å / % possible obs: 97.3 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.875 / Num. measured all: 72568 / Num. unique obs: 11096 / CC1/2: 0.882 / Rpim(I) all: 0.37 / Rrim(I) all: 0.951 / Χ2: 0.74 / Net I/σ(I) obs: 2.3

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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: 2→34.67 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 1997 4.65 %
Rwork0.1741 --
obs0.1757 42914 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→34.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4586 0 4 509 5099
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.2461380.1912883X-RAY DIFFRACTION98
2.05-2.110.22071420.18372897X-RAY DIFFRACTION98
2.11-2.170.23481410.17882885X-RAY DIFFRACTION98
2.17-2.240.23141410.1872906X-RAY DIFFRACTION98
2.24-2.320.26141410.19272898X-RAY DIFFRACTION99
2.32-2.410.23231430.192905X-RAY DIFFRACTION99
2.41-2.520.23951430.19312919X-RAY DIFFRACTION99
2.52-2.650.20851410.19022897X-RAY DIFFRACTION99
2.65-2.820.22561440.19552959X-RAY DIFFRACTION99
2.82-3.040.21861440.18952920X-RAY DIFFRACTION99
3.04-3.340.22511420.18322933X-RAY DIFFRACTION99
3.34-3.820.18341450.14972957X-RAY DIFFRACTION99
3.82-4.810.16071430.14982948X-RAY DIFFRACTION99
4.82-34.670.20251490.16653010X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 15.5669 Å / Origin y: -20.5816 Å / Origin z: -16.2712 Å
111213212223313233
T0.2042 Å20.0007 Å20.0011 Å2-0.1758 Å20.0027 Å2--0.1952 Å2
L0.0662 °2-0.0376 °2-0.0731 °2-0.021 °20.0242 °2--0.3181 °2
S-0.0096 Å °-0.011 Å °0.01 Å °0.0418 Å °-0.0087 Å °-0.013 Å °0.0188 Å °0.0431 Å °-0 Å °
Refinement TLS groupSelection details: all

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