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- PDB-6l2m: The structure of the tRNA-specific deaminase mutant from M. capricolum -
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Open data
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Basic information
Entry | Database: PDB / ID: 6l2m | ||||||
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Title | The structure of the tRNA-specific deaminase mutant from M. capricolum | ||||||
![]() | Nucleoside deaminase family protein | ||||||
![]() | RNA BINDING PROTEIN / tRNA-specific deaminase / protein engineering | ||||||
Function / homology | Cytidine and deoxycytidylate deaminase zinc-binding region / 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 / hydrolase activity / zinc ion binding / Nucleoside deaminase family protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xie, W. / Liu, H. / Wu, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of a tRNA-specific deaminase with compromised deamination activity. Authors: Liu, H. / Wu, S. / Ran, D. / Xie, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.4 KB | Display | ![]() |
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PDB format | ![]() | 29.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 9.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6l2lSC 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17683.342 Da / Num. of mol.: 1 Mutation: I19A,K20Q,H21L,N22G,S105D,Y106P,K146A, DEL(108-110) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MCGM508_01875 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.06 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.4M ammonium sulfate, 0.1M Sodium citrate pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 9158 / % possible obs: 100 % / Redundancy: 18.7 % / Biso Wilson estimate: 42.6410606465 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.105 / Net I/σ(I): 38.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 18.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 889 / CC1/2: 0.969 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6L2L Resolution: 2.30254929158→48.141486171 Å / SU ML: 0.292331904948 / Cross valid method: FREE R-VALUE / σ(F): 1.38105400115 / Phase error: 27.1589106138 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.0589077702 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.30254929158→48.141486171 Å
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Refine LS restraints |
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LS refinement shell |
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