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- PDB-1r5t: The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1r5t | ||||||
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Title | The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to U editase from Yeast | ||||||
![]() | Cytidine deaminase | ||||||
![]() | HYDROLASE / Zinc Dependent Deaminase / RNA editing / APOBEC-1 related protein | ||||||
Function / homology | ![]() Pyrimidine salvage / cytidine catabolic process / deoxycytidine catabolic process / cytidine deaminase / pyrimidine-containing compound salvage / cytidine deamination / cytidine deaminase activity / Neutrophil degranulation / zinc ion binding / identical protein binding ...Pyrimidine salvage / cytidine catabolic process / deoxycytidine catabolic process / cytidine deaminase / pyrimidine-containing compound salvage / cytidine deamination / cytidine deaminase activity / Neutrophil degranulation / zinc ion binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xie, K. / Sowden, M.P. / Dance, G.S.C. / Torelli, A.T. / Smith, H.C. / Wedekind, J.E. | ||||||
![]() | ![]() 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: ![]() Title: Activation induced deaminase: the importance of being specific Authors: Smith, H.C. / Bottaro, A. / Sowden, M.P. / Wedekind, J.E. #2: ![]() 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: ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.5 KB | Display | ![]() |
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PDB format | ![]() | 95.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.8 KB | Display | ![]() |
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Full document | ![]() | 469.2 KB | Display | |
Data in XML | ![]() | 26.3 KB | Display | |
Data in CIF | ![]() | 36.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | CDD1 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 | Mass: 15552.046 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Cdd1p / Plasmid: pET28a / Production host: ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.22 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction |
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: APS-1 / Detector: CCD / Date: Sep 17, 2001 / Details: Vertical Focusing Mirrors | ||||||||||||
Radiation | Monochromator: Si-111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.9708 Å2 / ksol: 0.319008 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
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Xplor file |
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