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- PDB-1r5t: The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to ... -

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Basic information

Entry
Database: PDB / ID: 1r5t
TitleThe Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to U editase from Yeast
ComponentsCytidine deaminase
KeywordsHYDROLASE / Zinc Dependent Deaminase / RNA editing / APOBEC-1 related protein
Function / homology
Function and homology information


Pyrimidine salvage / cytidine catabolic process / deoxycytidine catabolic process / pyrimidine-containing compound salvage / cytidine deaminase / cytidine deamination / cytidine deaminase activity / Neutrophil degranulation / zinc ion binding / identical protein binding ...Pyrimidine salvage / cytidine catabolic process / deoxycytidine catabolic process / pyrimidine-containing compound salvage / cytidine deaminase / cytidine deamination / cytidine deaminase activity / Neutrophil degranulation / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cytidine deaminase, homotetrameric / 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsXie, K. / Sowden, M.P. / Dance, G.S.C. / Torelli, A.T. / Smith, H.C. / Wedekind, J.E.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activation-induced deaminase and APOBEC-1.
Authors: Xie, K. / Sowden, M.P. / Dance, G.S. / Torelli, A.T. / Smith, H.C. / Wedekind, J.E.
#1: Journal: Trends Genet. / Year: 2004
Title: Activation induced deaminase: the importance of being specific
Authors: Smith, H.C. / Bottaro, A. / Sowden, M.P. / Wedekind, J.E.
#2: Journal: Trends Genet. / Year: 2003
Title: Messenger RNA editing in mammals: new members of the APOBEC family seeking roles in the family business
Authors: Wedekind, J.E. / Dance, G.S. / Sowden, M.P. / Smith, H.C.
#3: Journal: Nucleic Acids Res. / Year: 2001
Title: Identification of the Yeast Cytidine Deaminase CDD1 as an Orphan C-to-U RNA Editase
Authors: Dance, G.S. / Beemiller, P. / Yang, Y. / Mater, D.V. / Mian, I.S. / Smith, H.C.
#4: Journal: Nucleic Acids Res. / Year: 2000
Title: APOBEC-1 Dependent Cytidine to Uridine Editing of Apolipoprotein B RNA in Yeast
Authors: Dance, G.S. / Sowden, M.P. / Yang, Y. / Smith, H.C.
History
DepositionOct 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Cytidine deaminase
B: Cytidine deaminase
C: Cytidine deaminase
D: Cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4708
Polymers62,2084
Non-polymers2624
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10490 Å2
ΔGint-234 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.520, 86.370, 156.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-195-

HOH

21C-180-

HOH

DetailsCDD1 is a tetramer of identical subunits related by 222 symmetry. The asymmetric unit comprises 1 tetramer of chains A,B,C and D and includes four Zinc atoms.

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Components

#1: Protein
Cytidine deaminase / / Cytidine aminohydrolase / CDA


Mass: 15552.046 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Cdd1p / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus(TM) / References: UniProt: Q06549, cytidine 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 / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 5000 MME, ammonium chloride, sodium succinate, DTT, sodium azide, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.2574, 1.2831, 1.2828
DetectorType: APS-1 / Detector: CCD / Date: Sep 17, 2001 / Details: Vertical Focusing Mirrors
RadiationMonochromator: Si-111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.25741
21.28311
31.28281
ReflectionResolution: 2→29 Å / Num. all: 65372 / Num. obs: 63560 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 29.7 Å2 / Rsym value: 0.064 / Net I/σ(I): 17.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 5597 / Rsym value: 0.313 / % possible all: 74.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
SHELXphasing
DMphasing
Omodel building
RefinementMethod to determine structure: MAD / Resolution: 2→29.05 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 410906.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 5026 7.9 %RANDOM
Rwork0.188 ---
all0.191 65372 --
obs0.188 63560 91.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.9708 Å2 / ksol: 0.319008 e/Å3
Displacement parametersBiso mean: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å20 Å20 Å2
2--2.82 Å20 Å2
3----5.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 4 318 4517
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.752.5
X-RAY DIFFRACTIONc_scbond_it2.282.5
X-RAY DIFFRACTIONc_scangle_it3.993.5
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.28 512 7.9 %
Rwork0.237 5991 -
obs-5991 74.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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