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Yorodumi- PDB-4kdz: Crystal structure of tRNA/rRNA methyltransferase YibK from Escher... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kdz | ||||||
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Title | Crystal structure of tRNA/rRNA methyltransferase YibK from Escherichia coli (Target NYSGRC-012599) | ||||||
Components | tRNA (cytidine(34)-2'-O)-methyltransferase | ||||||
Keywords | TRANSFERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / SpoU methyltransferase / S-adenosyl-l-methionine | ||||||
Function / homology | Function and homology information tRNA (cytidine34-2'-O)-methyltransferase / tRNA methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Kim, J. / Toro, R. / Bhosle, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of tRNA/rRNA methyltransferase YibK from Escherichia coli (Target NYSGRC-012599) Authors: Kim, J. / Toro, R. / Bhosle, R. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kdz.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kdz.ent.gz | 31.1 KB | Display | PDB format |
PDBx/mmJSON format | 4kdz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/4kdz ftp://data.pdbj.org/pub/pdb/validation_reports/kd/4kdz | HTTPS FTP |
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-Related structure data
Related structure data | 3n4jS S: Starting model for refinement |
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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: 17747.225 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: UTI89 / Gene: b3606, JW3581, trmL, UTI89_C4147, yibK / Plasmid: LIC pET46a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q1R4Y9, tRNA (cytidine34-2'-O)-methyltransferase |
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#2: 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: 4.56 Å3/Da / Density % sol: 73.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES (pH7.5) 1.4M sodium citrate tribasic dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2011 |
Radiation | Monochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→50 Å / Num. all: 14445 / Num. obs: 14428 / % possible obs: 99.9 % / Redundancy: 9 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.32→2.36 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3N4J Resolution: 2.32→42.25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.993 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.503 Å2
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Refinement step | Cycle: LAST / Resolution: 2.32→42.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.319→2.379 Å / Total num. of bins used: 20
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