+Open data
-Basic information
Entry | Database: PDB / ID: 4gek | ||||||
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Title | Crystal Structure of wild-type CmoA from E.coli | ||||||
Components | tRNA (cmo5U34)-methyltransferase | ||||||
Keywords | TRANSFERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Rossmann fold / synthase / SAM prephenate | ||||||
Function / homology | Function and homology information Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / carboxyl- or carbamoyltransferase activity / tRNA wobble uridine modification / S-adenosyl-L-methionine binding / methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Kim, J. / Toro, R. / Bonanno, J.B. / Bhosle, R. / Sampathkumar, P. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: Nature / Year: 2013 Title: Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function Authors: Kim, J. / Xiao, H. / Bonanno, J.B. / Kalyanaraman, C. / Brown, S. / Tang, X. / Al-Obaidi, N.F. / Patskovsky, Y. / Babbitt, P.C. / Jacobson, M.P. / Lee, Y.-S. / 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 | 4gek.cif.gz | 120.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gek.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 4gek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/4gek ftp://data.pdbj.org/pub/pdb/validation_reports/ge/4gek | HTTPS FTP |
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-Related structure data
Related structure data | 1im8S 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 29544.537 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655 / Gene: cmoA / Plasmid: LIC pET46a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: C3T5M2*PLUS, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M Li2SO4, 0.1M Bis-Tris:HCl pH 5.5, 25% PEG3350, 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: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2012 |
Radiation | Monochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 76870 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 29.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IM8 Resolution: 1.5→44.18 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.185 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.075 / 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: 20.346 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→44.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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