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- PDB-2o3k: Yeast Cytosine Deaminase D92E Triple Mutant bound to transition s... -

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Basic information

Entry
Database: PDB / ID: 2o3k
TitleYeast Cytosine Deaminase D92E Triple Mutant bound to transition state analogue HPY
ComponentsCytosine deaminase
KeywordsHYDROLASE / Homodimer / Transition State Analogue
Function / homology
Function and homology information


cytidine metabolic process / diaminohydroxyphosphoribosylaminopyrimidine deaminase activity / cytosine deaminase / pyrimidine-containing compound salvage / : / 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
4-HYDROXY-3,4-DIHYDRO-1H-PYRIMIDIN-2-ONE / Cytosine deaminase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKorkegian, A.M. / Stoddard, B.L.
CitationJournal: To be Published
Title: Crystal structure of Yeast Cytosine Deaminase D92E Triple Mutant bound to transition state analogue HPY
Authors: Stolworthy, T. / Korkegian, A.M. / Willmon, C. / Stoddard, B.L. / Black, M.E.
History
DepositionDec 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)36,0627
Polymers35,6632
Non-polymers3995
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-90 kcal/mol
Surface area11970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.916, 69.090, 74.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytosine deaminase / Cytosine aminohydrolase


Mass: 17831.359 Da / Num. of mol.: 2 / Mutation: A23L, D92E, V108I, I140L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FCY1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL / 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-HPY / 4-HYDROXY-3,4-DIHYDRO-1H-PYRIMIDIN-2-ONE


Mass: 114.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6N2O2
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 23% PEG 8000, 0.1 M Sodium cacodylate, 0.1 M Calcium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2005
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 13334 / Num. obs: 13334 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.042 / Rsym value: 0.037 / Net I/σ(I): 8.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 7.5 / Rsym value: 0.078 / % possible all: 100

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Phasing

Phasing MRRfactor: 0.517 / Cor.coef. Fo:Fc: 0.587
Highest resolutionLowest resolution
Translation1.6 Å20 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YSB

1ysb


Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1355 10.2 %RANDOM
Rwork0.204 ---
obs0.204 13204 99.3 %-
all-13334 --
Solvent computationBsol: 59.535 Å2
Displacement parametersBiso mean: 17.572 Å2
Baniso -1Baniso -2Baniso -3
1--1.793 Å20 Å20 Å2
2--3.296 Å20 Å2
3----1.503 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 19 133 2548
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.1641.5
X-RAY DIFFRACTIONc_mcangle_it1.8132
X-RAY DIFFRACTIONc_scbond_it2.0152
X-RAY DIFFRACTIONc_scangle_it2.9052.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used
2.3-2.330.267500.206443X-RAY DIFFRACTION27
2.33-2.360.263480.198422X-RAY DIFFRACTION27
2.36-2.390.279430.209433X-RAY DIFFRACTION27
2.39-2.430.297600.209391X-RAY DIFFRACTION27
2.43-2.460.288580.212430X-RAY DIFFRACTION27
2.46-2.50.284430.206421X-RAY DIFFRACTION27
2.5-2.540.316530.22443X-RAY DIFFRACTION27
2.54-2.590.286610.196407X-RAY DIFFRACTION27
2.59-2.630.296430.202445X-RAY DIFFRACTION27
2.63-2.680.298580.225427X-RAY DIFFRACTION27
2.68-2.740.283400.219441X-RAY DIFFRACTION27
2.74-2.80.296500.203433X-RAY DIFFRACTION27
2.8-2.860.237470.209424X-RAY DIFFRACTION27
2.86-2.930.229410.188443X-RAY DIFFRACTION27
2.93-3.010.324330.194449X-RAY DIFFRACTION27
3.01-3.10.254430.229455X-RAY DIFFRACTION27
3.1-3.20.264560.213432X-RAY DIFFRACTION27
3.2-3.320.243540.196434X-RAY DIFFRACTION27
3.32-3.450.243460.194436X-RAY DIFFRACTION27
3.45-3.610.271700.201426X-RAY DIFFRACTION27
3.61-3.80.209450.178439X-RAY DIFFRACTION27
3.8-4.030.212450.193470X-RAY DIFFRACTION27
4.03-4.350.23550.192430X-RAY DIFFRACTION27
4.35-4.780.221560.166453X-RAY DIFFRACTION27
4.78-5.470.185460.187460X-RAY DIFFRACTION27
5.47-6.890.267550.239467X-RAY DIFFRACTION27
6.89-500.311560.269495X-RAY DIFFRACTION27
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water.param
X-RAY DIFFRACTION4dhp.param

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