+Open data
-Basic information
Entry | Database: PDB / ID: 6l2l | ||||||
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Title | The structure of the tRNA-specific deaminase from M. capricolum | ||||||
Components | Nucleoside deaminase family protein | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Mycoplasma capricolum subsp. capricolum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.40045827641 Å | ||||||
Authors | Xie, W. / Liu, H. / Wu, S. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem.J. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l2l.cif.gz | 53.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l2l.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 6l2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/6l2l ftp://data.pdbj.org/pub/pdb/validation_reports/l2/6l2l | HTTPS FTP |
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-Related structure data
Related structure data | 6l2mC 2a8nS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18222.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma capricolum subsp. capricolum (bacteria) Gene: MCGM508_01875 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C2W6A5 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 0.49M sodium phosphate monobasic monohydrate, 0.91M potassium phosphate dibasic, pH 6.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: May 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→21.07 Å / Num. obs: 7697 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 30.8505494456 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1081 / CC1/2: 0.884 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2A8N Resolution: 2.40045827641→21.0651823974 Å / SU ML: 0.283284022304 / Cross valid method: FREE R-VALUE / σ(F): 1.35523401539 / Phase error: 22.7719217549 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: 37.4680633037 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.40045827641→21.0651823974 Å
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Refine LS restraints |
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LS refinement shell |
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