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- PDB-1uaq: The crystal structure of yeast cytosine deaminase -

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Basic information

Entry
Database: PDB / ID: 1uaq
TitleThe crystal structure of yeast cytosine deaminase
Componentscytosine deaminase
KeywordsHYDROLASE / alpha-beta-alpha
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 / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE / Cytosine deaminase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsKo, T.-P. / Lin, J.-J. / Hu, C.-Y. / Hsu, Y.-H. / Wang, A.H.-J. / Liaw, S.-H.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of yeast cytosine deaminase. Insights into enzyme mechanism and evolution
Authors: Ko, T.-P. / Lin, J.-J. / Hu, C.-Y. / Hsu, Y.-H. / Wang, A.H.-J. / Liaw, S.-H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and preliminary crystallographic analysis of yeast cytosine deaminase
Authors: Hsu, Y.-H. / Hu, C.-Y. / Lin, J.-J. / Liaw, S.-H.
History
DepositionMar 14, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)35,4196
Polymers35,0602
Non-polymers3594
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-85 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.113, 53.681, 68.076
Angle α, β, γ (deg.)90.00, 105.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein cytosine deaminase


Mass: 17530.018 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: fcy1 / Plasmid: pET-6H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: Q12178, cytosine deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DUC / DIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE / DIHYDROURACIL


Mass: 114.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: isopropanol, PEG4000, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Details: Hsu, Y.-H., (2003) Acta Crystallogr., Sect.D, 59, 950.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %2-propanol1reservoir
220 %PEG40001reservoir
30.1 Msodium HEPES1reservoirpH7.5
430 mg/mlprotein1drop
50-20 mM2-hydroxypyrimidine1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.71 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 3, 2002
RadiationMonochromator: the rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 42187 / Num. obs: 42187 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.066 / Rsym value: 0.057 / Net I/σ(I): 11.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3945 / Rsym value: 0.297 / % possible all: 91.2
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 277542
Reflection shell
*PLUS
Highest resolution: 1.6 Å / % possible obs: 91.2 % / Num. unique obs: 3945 / Num. measured obs: 18894 / Rmerge(I) obs: 0.338

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.6→23.79 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1095 -RANDOM
Rwork0.177 ---
all0.178 43400 --
obs0.177 38222 88.1 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.161 Å20 Å27.895 Å2
2--0.223 Å20 Å2
3----0.063 Å2
Refine analyzeLuzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.6→23.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 18 484 2858
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 1.6→1.66 Å /
Num. reflection% reflection
Rfree1905 -
obs18894 91.2 %
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Rfactor Rfree: 0.313 / Rfactor Rwork: 0.268 / Num. reflection obs: 3157

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