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Yorodumi- PDB-1uam: Crystal structure of tRNA(m1G37)methyltransferase: Insight into t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uam | ||||||
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Title | Crystal structure of tRNA(m1G37)methyltransferase: Insight into tRNA recognition | ||||||
Components | tRNA (Guanine-N(1)-)-methyltransferase | ||||||
Keywords | TRANSFERASE / methyltransferase / SPOUT class / trmD / tRNA(m1G37)methyltransferase / tRNA modification | ||||||
Function / homology | Function and homology information tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / cytosol Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ahn, H.J. / Kim, H.-W. / Yoon, H.-J. / Lee, B.I. / Suh, S.W. / Yang, J.K. | ||||||
Citation | Journal: EMBO J. / Year: 2003 Title: Crystal structure of tRNA(m(1)G37)methyltransferase: insights into tRNA recognition Authors: Ahn, H.J. / Kim, H.-W. / Yoon, H.-J. / Lee, B.I. / Suh, S.W. / Yang, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uam.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uam.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 1uam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uam_validation.pdf.gz | 803.5 KB | Display | wwPDB validaton report |
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Full document | 1uam_full_validation.pdf.gz | 807.9 KB | Display | |
Data in XML | 1uam_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 1uam_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/1uam ftp://data.pdbj.org/pub/pdb/validation_reports/ua/1uam | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30821.154 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P43912, EC: 2.1.1.31 |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-SAH / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 50.95 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: sodium citrate, ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 10, 2002 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 39786 / Num. obs: 15004 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 25.3 Å2 / Rsym value: 0.069 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.262 / % possible all: 91.6 |
Reflection | *PLUS Num. measured all: 39786 / Rmerge(I) obs: 0.069 |
Reflection shell | *PLUS % possible obs: 91.6 % / Rmerge(I) obs: 0.262 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2744283.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 76.4563 Å2 / ksol: 0.446046 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.303 / Rfactor Rwork: 0.267 |