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- PDB-6zmc: Structure of the tRNA-Monooxygenase enzyme MiaE frozen under 2000... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zmc | ||||||
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Title | Structure of the tRNA-Monooxygenase enzyme MiaE frozen under 2000 bar using the high pressure freezing method | ||||||
![]() | tRNA hydroxylase | ||||||
![]() | OXIDOREDUCTASE / tRNA-monooxygenase metallo-enzyme tRNA-modifying enzyme hydroxylase | ||||||
Function / homology | ![]() tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine)-hydroxylase activity / tRNA modification / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Carpentier, P. / Atta, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural, biochemical and functional analyses of tRNA-monooxygenase enzyme MiaE from Pseudomonas putida provide insights into tRNA/MiaE interaction. Authors: Carpentier, P. / Lepretre, C. / Basset, C. / Douki, T. / Torelli, S. / Duarte, V. / Hamdane, D. / Fontecave, M. / Atta, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.5 KB | Display | ![]() |
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PDB format | ![]() | 74.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6zmaC ![]() 6zmbC ![]() 2itbS 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, 2 molecules BC
#1: Protein | Mass: 22661.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 8 types, 65 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/AR.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/AR.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-CL / | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-AR / | #8: Chemical | ChemComp-PEG / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.75 % / Description: elongated |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: protein : 20 mg/ml in 100 mM HEPES, pH 7.5, 30 mM NaCl reservoir : 0.5 M CaCl2, 42% PEG 6k, 2 M Tris-Cl pH 8 |
-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: Jun 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.77 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 16699 / % possible obs: 99.3 % / Observed criterion σ(I): 2.2 / Redundancy: 6.2 % / Biso Wilson estimate: 72.2 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.065 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.5→2.65 Å / Redundancy: 6.01 % / Mean I/σ(I) obs: 2.24 / Num. unique obs: 2618 / CC1/2: 0.912 / Rrim(I) all: 0.79 / % possible all: 97.7 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2ITB Resolution: 2.5→47.52 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 12.289 / SU ML: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.47 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 144.51 Å2 / Biso mean: 69.561 Å2 / Biso min: 47.47 Å2
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Refinement step | Cycle: final / Resolution: 2.5→47.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 Å / Rfactor Rfree error: 0
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