+Open data
-Basic information
Entry | Database: PDB / ID: 6zmb | ||||||
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Title | Structure of the native tRNA-Monooxygenase enzyme MiaE | ||||||
Components | tRNA hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / tRNA-monooxygenase metallo-enzyme tRNA-modifying enzyme hydroxylase | ||||||
Function / homology | Function and homology information tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine)-hydroxylase activity / tRNA modification / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida KT2440 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Carpentier, P. / Atta, M. | ||||||
Funding support | France, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zmb.cif.gz | 105.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zmb.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 6zmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zmb_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 6zmb_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 6zmb_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 6zmb_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/6zmb ftp://data.pdbj.org/pub/pdb/validation_reports/zm/6zmb | HTTPS FTP |
-Related structure data
Related structure data | 6zmaC 6zmcC 2itbS 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 on special symmetry positions |
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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.) Pseudomonas putida KT2440 (bacteria) / Gene: AYO08_21560, CBL13_00280, CBP06_18695 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A179QS89 |
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-Non-polymers , 9 types, 232 molecules
#2: Chemical | ChemComp-FE / #3: Chemical | #4: Chemical | ChemComp-CA / | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-PG4 / | #8: Chemical | #9: Chemical | ChemComp-PG6 / | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.93 % / Description: elongated |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: MiaE: 20 mg/ml in 100 mM HEPES, pH 7.5, 30mM NaCl reservoir solution: 0.5M CaCl2, 42% PEG 6k, 2M Tris-Cl pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9753 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9753 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 48290 / % possible obs: 97.5 % / Observed criterion σ(I): 1.44 / Redundancy: 2.8 % / Biso Wilson estimate: 38.8 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.04 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 2.8 % / Num. unique obs: 7733 / CC1/2: 0.845 / Rrim(I) all: 0.846 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ITB Resolution: 1.7→46.752 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.89 / Stereochemistry target values: ML
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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 max: 92.64 Å2 / Biso mean: 36.955 Å2 / Biso min: 18.88 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→46.752 Å
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LS refinement shell | Resolution: 1.7→1.73 Å /
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