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- PDB-1ysb: Yeast Cytosine Deaminase Triple Mutant -

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Basic information

Entry
Database: PDB / ID: 1ysb
TitleYeast Cytosine Deaminase Triple Mutant
ComponentsCytosine deaminase
KeywordsHYDROLASE
Function / homology
Function and homology information


cytidine metabolic process / pyrimidine-containing compound salvage / ec:3.5.4.1: / 5-fluorocytosine deaminase activity / cytosine deaminase activity / UMP salvage / cytosine metabolic process / zinc ion binding / nucleus / cytoplasm
Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine deaminase-like / APOBEC/CMP deaminase, zinc-binding
Cytosine deaminase
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKorkegian, A. / Black, M.E. / Baker, D. / Stoddard, B.L.
CitationJournal: Science / Year: 2005
Title: Computational thermostabilization of an enzyme.
Authors: Korkegian, A. / Black, M.E. / Baker, D. / Stoddard, B.L.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 8, 2005 / Release: May 17, 2005
RevisionDateData content typeGroupProviderType
1.0May 17, 2005Structure modelrepositoryInitial release
1.1Apr 30, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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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)35,9367
Polymers35,6352
Non-polymers3025
Water7,152397
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-175 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)39.52, 54.63, 68.12
Angle α, β, γ (deg.)90.00, 105.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Cytosine deaminase / / Cytosine aminohydrolase


Mass: 17817.334 Da / Num. of mol.: 2 / Mutation: A23L, V108I, I140L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: FCY1 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL / References: UniProt: Q12178, EC: 3.5.4.1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Zinc
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Calcium
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 1.99 Å3/Da / Density % sol: 38.2 %
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 22, 2004
RadiationMonochromator: OSMIC DIFFRACTION GRATING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 29093 / % possible obs: 93.9 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 19
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 9.5 / % possible all: 86.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→50 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.189 2874 RANDOM
Rwork0.162 --
Obs0.162 28869 -
All-28869 -
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 5 397 2853
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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