+Open data
-Basic information
Entry | Database: PDB / ID: 7e3q | ||||||
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Title | Crystal structure of SAH bound TrmL from Vibrio vulnificus | ||||||
Components | tRNA (cytidine(34)-2'-O)-methyltransferase | ||||||
Keywords | TRANSFERASE / tRNA modification / methyltransferase / SAM / SAH / tRNA_Leu / cytidine/uridine-2'-O-methyltransferase | ||||||
Function / homology | Function and homology information tRNA (cytidine34-2'-O)-methyltransferase / tRNA methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Vibrio vulnificus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Kim, J. / Son, J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: Crystal structure of SAH bound TrmL from Vibrio vulnificus Authors: Kim, J. / Son, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e3q.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e3q.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 7e3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/7e3q ftp://data.pdbj.org/pub/pdb/validation_reports/e3/7e3q | HTTPS FTP |
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-Related structure data
Related structure data | 4kdzS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 1 - 158 / Label seq-ID: 1 - 158
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-Components
#1: Protein | Mass: 18828.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: MO6-24/O / Gene: trmL, CRN52_04235 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A1W6M7K7, tRNA (cytidine34-2'-O)-methyltransferase #2: Chemical | ChemComp-SAH / | #3: Water | ChemComp-HOH / | 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: 2.29 Å3/Da / Density % sol: 46.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-hydrochloride pH 8.5, 0.2M Magnesium chloride hexahydrate, 30% w/v PEG 4000, 40% v/v tert-Butano |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 28, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 9778 / % possible obs: 99.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.081 / Rrim(I) all: 0.22 / Χ2: 0.72 / Net I/σ(I): 2.9 / Num. measured all: 67737 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KDZ Resolution: 2.7→49.49 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.915 / SU B: 14.322 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.36 / 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: 103.47 Å2 / Biso mean: 34.985 Å2 / Biso min: 2.65 Å2
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Refinement step | Cycle: final / Resolution: 2.7→49.49 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 4399 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.701→2.771 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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