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Open data
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Basic information
Entry | Database: PDB / ID: 4lcp | ||||||
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Title | Crytsal structure of NE0047 in complex with 2,6-diaminopurine | ||||||
![]() | 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 | ![]() | 83.9 KB | Display | ![]() |
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PDB format | ![]() | 63.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.8 KB | Display | ![]() |
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Full document | ![]() | 458.8 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lc5C ![]() 4lcnC ![]() 4lcoC ![]() 4ld2C ![]() 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-6AP / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.07 % |
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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 5.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction source | Source: ![]() |
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Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 21220 / Num. obs: 21220 / % possible obs: 96.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 25.2 / % possible all: 94.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2G84 Resolution: 2→33.95 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.698 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.39 Å2 / Biso mean: 24.386 Å2 / Biso min: 10.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2→33.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.052 Å / Total num. of bins used: 20
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