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Yorodumi- PDB-8sh4: Crystal structure of the tRNA (m1G37) methyltransferase apoenzyme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sh4 | ||||||||||||
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Title | Crystal structure of the tRNA (m1G37) methyltransferase apoenzyme from Anaplasma phagocytophilum | ||||||||||||
Components | tRNA (guanine-N(1)-)-methyltransferase | ||||||||||||
Keywords | TRANSFERASE / methyltransferase / apoenzyme / TrmD / SPOUT | ||||||||||||
Function / homology | Function and homology information tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Anaplasma phagocytophilum (agent of human granulocytic ehrlichiosis) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||||||||
Authors | Jannotta, C. / Edele, D. / Levanti, D. / Carson, M. / Prucha, G. / Caesar, J. / Picchiello, C. / Collins, K. / Garland, E. / Handley-Pendleton, J. ...Jannotta, C. / Edele, D. / Levanti, D. / Carson, M. / Prucha, G. / Caesar, J. / Picchiello, C. / Collins, K. / Garland, E. / Handley-Pendleton, J. / Hernandez, V. / Leffler, S. / Williams, D. / Stojanoff, V. / Perez, A. / Halloran, J. / Bolen, R. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Crystal structure of the m1G37 tRNA methyltransferase apoenzyme from Anaplasma phagocytophilum Authors: Jannotta, C. / Edele, D. / Levanti, D. / Carson, M. / Prucha, G. / Caesar, J. / Collins, K. / Garland, E. / Handley-Pendleton, J. / Hernandez, V. / Leffler, S. / Williams, D. / Stojanoff, V. ...Authors: Jannotta, C. / Edele, D. / Levanti, D. / Carson, M. / Prucha, G. / Caesar, J. / Collins, K. / Garland, E. / Handley-Pendleton, J. / Hernandez, V. / Leffler, S. / Williams, D. / Stojanoff, V. / Perez, A. / Halloran, J. / Bolen, R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sh4.cif.gz | 88.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sh4.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 8sh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sh4_validation.pdf.gz | 436.5 KB | Display | wwPDB validaton report |
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Full document | 8sh4_full_validation.pdf.gz | 438.8 KB | Display | |
Data in XML | 8sh4_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 8sh4_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/8sh4 ftp://data.pdbj.org/pub/pdb/validation_reports/sh/8sh4 | HTTPS FTP |
-Related structure data
Related structure data | 3knuS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24069.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anaplasma phagocytophilum (agent of human granulocytic ehrlichiosis) Gene: trmD / Production host: Escherichia coli (E. coli) / References: UniProt: A0A182A739 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.83 Å3/Da / Density % sol: 74.56 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 8% PEG 3350, 0.5mL of 0.1M sodium citrate, 10% glycerol, ethylene glycol as cryoprotectant |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 2.676→34.4 Å / Num. obs: 11321 / % possible obs: 88.49 % / Redundancy: 15.5 % / Biso Wilson estimate: 77.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.676→2.854 Å / Num. unique obs: 566 / CC1/2: 0.535 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KNU Resolution: 2.9→34.4 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.07 / 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 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→34.4 Å
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Refine LS restraints |
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LS refinement shell |
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