+Open data
-Basic information
Entry | Database: PDB / ID: 5gra | ||||||
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Title | Crystal structure of TrmJ from Z. mobilis ZM4 | ||||||
Components | tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ | ||||||
Keywords | TRANSFERASE / methyltransferase / tRNA / TrmJ | ||||||
Function / homology | Function and homology information tRNA (cytidine32/uridine32-2'-O)-methyltransferase / RNA methyltransferase activity / tRNA processing / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.005 Å | ||||||
Authors | Gu, D.-H. / Kim, J.-S. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: An asymmetric dimeric structure of TrmJ tRNA methyltransferase from Zymomonas mobilis with a flexible C-terminal dimer Authors: Gu, D.-H. / Park, M.-Y. / Kim, J.-S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gra.cif.gz | 186.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gra.ent.gz | 150.8 KB | Display | PDB format |
PDBx/mmJSON format | 5gra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gra_validation.pdf.gz | 435.2 KB | Display | wwPDB validaton report |
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Full document | 5gra_full_validation.pdf.gz | 444.9 KB | Display | |
Data in XML | 5gra_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 5gra_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/5gra ftp://data.pdbj.org/pub/pdb/validation_reports/gr/5gra | HTTPS FTP |
-Related structure data
Similar structure data |
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-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
#1: Protein | Mass: 26466.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria) Strain: ATCC 31821 / ZM4 / CP4 / Gene: trmJ, ZMO1203 / Production host: Escherichia coli (E. coli) References: UniProt: Q5NN83, tRNA (cytidine32/uridine32-2'-O)-methyltransferase #2: Water | ChemComp-HOH / | |
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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: 2.5 Å3/Da / Density % sol: 50.76 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: Ammonium Sulfate, MES, Lithium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97952 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97952 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 19496 / % possible obs: 97.7 % / Redundancy: 1.8 % / Net I/σ(I): 4.1 |
-Processing
Software |
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Refinement | Resolution: 3.005→40.656 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.005→40.656 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 43.5687 Å / Origin y: -22.5466 Å / Origin z: 52.58 Å
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Refinement TLS group | Selection details: all |