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Yorodumi- PDB-1mxi: Structure of YibK from Haemophilus influenzae (HI0766): a Methylt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mxi | ||||||
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Title | Structure of YibK from Haemophilus influenzae (HI0766): a Methyltransferase with a Cofactor Bound at a Site Formed by a Knot | ||||||
Components | Hypothetical tRNA/rRNA methyltransferase HI0766 | ||||||
Keywords | TRANSFERASE / methyltransferase / S-adenosylhomocysteine / spoU family / Structure 2 Function Project / S2F / Structural Genomics | ||||||
Function / homology | Function and homology information tRNA (cytidine(34)-2'-O)-methyltransferase activity / tRNA (5-carboxymethylaminomethyluridine(34)-2'-O)-methyltransferase activity / wobble position cytosine ribose methylation / wobble position uridine ribose methylation / tRNA (cytidine34-2'-O)-methyltransferase / RNA binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Lim, K. / Zhang, H. / Tempczyk, A. / Bonander, N. / Toedt, J. / Howard, A. / Eisenstein, E. / Herzberg, O. / Structure 2 Function Project (S2F) | ||||||
Citation | Journal: Proteins / Year: 2003 Title: Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a Cofactor Bound at a Site Formed by a Knot Authors: Lim, K. / Zhang, H. / Tempczyk, A. / Krajewski, W. / Bonander, N. / Toedt, J. / Howard, A. / Eisenstein, E. / Herzberg, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mxi.cif.gz | 49.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mxi.ent.gz | 34.9 KB | Display | PDB format |
PDBx/mmJSON format | 1mxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/1mxi ftp://data.pdbj.org/pub/pdb/validation_reports/mx/1mxi | HTTPS FTP |
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-Related structure data
Related structure data | 1j85SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
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: 18427.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI0766 / Plasmid: PET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P44868, Transferases; Transferring one-carbon groups; Methyltransferases |
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#2: Chemical | ChemComp-IOD / |
#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: 1.87 Å3/Da / Density % sol: 34.27 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K Method: vapor diffusion, hanging drop, soaking of crystal with cofactor sah pH: 4.6 Details: 20% PMME 2000, 0.1 M sodium acetate, 0.2 M ammonium acetate, 3 % ethylene glycol, pH 4.6, Vapor diffusion, hanging drop, soaking of crystal with cofactor SAH, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 15394 / Num. obs: 15394 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.7→1.78 Å / Rmerge(I) obs: 0.223 / % possible all: 69.2 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 281315 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / % possible obs: 69.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 1j85 Resolution: 1.7→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 29 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.78 Å / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.215 |