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Yorodumi- PDB-7kff: Crystal structure of TrmD tRNA (guanine-N1)-methyltransferase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kff | ||||||
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Title | Crystal structure of TrmD tRNA (guanine-N1)-methyltransferase from Corynebacterium diphtheriae in complex with SAH | ||||||
Components | tRNA (guanine-N(1)-)-methyltransferase | ||||||
Keywords | TRANSFERASE / CSGID / knot / Center for Structural Genomics of Infectious Diseases | ||||||
Function / homology | Function and homology information tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Corynebacterium diphtheriae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å | ||||||
Authors | Michalska, K. / Tanase, L. / Maltseva, N. / Kim, Y. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of TrmD tRNA (guanine-N1)-methyltransferase from Corynebacterium diphtheriae in complex with SAH Authors: Michalska, K. / Tanase, L. / Maltseva, N. / Kim, Y. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kff.cif.gz | 198.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kff.ent.gz | 138.1 KB | Display | PDB format |
PDBx/mmJSON format | 7kff.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kff_validation.pdf.gz | 817 KB | Display | wwPDB validaton report |
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Full document | 7kff_full_validation.pdf.gz | 819.2 KB | Display | |
Data in XML | 7kff_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 7kff_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/7kff ftp://data.pdbj.org/pub/pdb/validation_reports/kf/7kff | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34815.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: trmD, BT093_03755, CIP107518_01276 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A2T1BS25, UniProt: Q6NGI5*PLUS, tRNA (guanine37-N1)-methyltransferase |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-SAH / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.08 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.17 M sodium acetate, 0.085 M Tris/HCl pH 8.5, 25.5% PEG 4000, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 16, 2019 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. obs: 70894 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 15.96 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.109 / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.417 / Mean I/σ(I) obs: 1.71 / Num. unique obs: 3365 / CC1/2: 0.577 / CC star: 0.855 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.35→28.79 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.2558 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: 27.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→28.79 Å
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Refine LS restraints |
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LS refinement shell |
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