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- PDB-7oqx: Crystal structure of a psychrophilic CCA-adding enzyme in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7oqx | |||||||||
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Title | Crystal structure of a psychrophilic CCA-adding enzyme in complex with CMPcPP | |||||||||
![]() | CCA-adding enzyme | |||||||||
![]() | RNA BINDING PROTEIN / tRNA maturation / tRNA nucleotidyltransferase / psychrophilic enzyme | |||||||||
Function / homology | ![]() tRNA 3'-terminal CCA addition / nucleotidyltransferase activity / tRNA binding / nucleotide binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rollet, K. / de Wijn, R. / Bluhm, A. / Hennig, O. / Betat, H. / Moerl, M. / Lorber, B. / Sauter, C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: CCA-addition in the cold: Structural characterization of the psychrophilic CCA-adding enzyme from the permafrost bacterium Planococcus halocryophilus . Authors: de Wijn, R. / Rollet, K. / Ernst, F.G.M. / Wellner, K. / Betat, H. / Morl, M. / Sauter, 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 | ![]() | 106.5 KB | Display | ![]() |
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PDB format | ![]() | 73.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7otlC ![]() 7otrC ![]() 6qxnS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48498.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 112 molecules ![](data/chem/img/2TM.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-2TM / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.37 % / Description: bipyramid |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: protein solution at 4.5 mg/mL in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 5 mM MgCl2; reservoir solution: 100 mM Sodium acetate; pH 4.5 1 M di-Ammonium hydrogen phosphate remarks : soaking 30 ...Details: protein solution at 4.5 mg/mL in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 5 mM MgCl2; reservoir solution: 100 mM Sodium acetate; pH 4.5 1 M di-Ammonium hydrogen phosphate remarks : soaking 30 seconds in a drop with 10 mM CMPcPP and reservoir solution + 20% glycerol PH range: 4.5 - 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 37711 / % possible obs: 99.8 % / Redundancy: 25.7 % / Biso Wilson estimate: 50.85 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.15 / Net I/av σ(I): 16.84 / Net I/σ(I): 16.84 |
Reflection shell | Resolution: 2.2→2.34 Å / Redundancy: 27.1 % / Mean I/σ(I) obs: 1.98 / Num. unique obs: 5903 / CC1/2: 0.786 / Rrim(I) all: 1.616 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6QXN Resolution: 2.2→46.74 Å / SU ML: 0.2954 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6168 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: 51.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→46.74 Å
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Refine LS restraints |
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LS refinement shell |
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