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Open data
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Basic information
Entry | Database: PDB / ID: 4ld2 | ||||||
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Title | Crystal structure of NE0047 in complex with cytidine | ||||||
![]() | Cytidine and deoxycytidylate deaminase zinc-binding region | ||||||
![]() | HYDROLASE / CDA fold / deaminase | ||||||
Function / homology | ![]() guanosine deaminase activity / purine nucleoside catabolic process / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bitra, A. / Biswas, A. / Anand, R. | ||||||
![]() | ![]() Title: Structural basis of the substrate specificity of cytidine deaminase superfamily Guanine deaminase Authors: Bitra, A. / Biswas, A. / Anand, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.3 KB | Display | ![]() |
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PDB format | ![]() | 63.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.6 KB | Display | ![]() |
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Full document | ![]() | 473 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lc5C ![]() 4lcnC ![]() 4lcoC ![]() 4lcpC ![]() 4ld4C ![]() 2g84S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20586.463 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q82Y41, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds #2: Chemical | #3: Chemical | ChemComp-CTN / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.42 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.225M MgCl2, 25% PEG 3350, 0.1M Bis-Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.55→27.53 Å / Num. all: 46602 / Num. obs: 46602 / % possible obs: 100 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 4.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2G84 Resolution: 1.55→27.53 Å / Occupancy max: 1 / Occupancy min: 0.3 / σ(F): 0
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Solvent computation | Bsol: 35.2375 Å2 | ||||||||||||||||||
Displacement parameters | Biso max: 69.57 Å2 / Biso mean: 16.1116 Å2 / Biso min: 1.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→27.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Rfactor Rfree error: 0.086 / Total num. of bins used: 20 /
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Xplor file |
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