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Yorodumi- PDB-4iwn: Crystal structure of a putative methyltransferase CmoA in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iwn | ||||||
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Title | Crystal structure of a putative methyltransferase CmoA in complex with a novel SAM derivative | ||||||
Components | tRNA (cmo5U34)-methyltransferase | ||||||
Keywords | TRANSFERASE / putative tRNA modification enzyme / SCM-SAH | ||||||
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 / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å | ||||||
Authors | Aller, P. / Lobley, C.M. / Byrne, R.T. / Antson, A.A. / Waterman, D.G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: S-Adenosyl-S-carboxymethyl-L-homocysteine: a novel cofactor found in the putative tRNA-modifying enzyme CmoA. Authors: Byrne, R.T. / Whelan, F. / Aller, P. / Bird, L.E. / Dowle, A. / Lobley, C.M. / Reddivari, Y. / Nettleship, J.E. / Owens, R.J. / Antson, A.A. / Waterman, D.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iwn.cif.gz | 198.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iwn.ent.gz | 157.8 KB | Display | PDB format |
PDBx/mmJSON format | 4iwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/4iwn ftp://data.pdbj.org/pub/pdb/validation_reports/iw/4iwn | 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 |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25732.246 Da / Num. of mol.: 2 / Fragment: UNP residues 19-247 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cmoA, yecO, b1870, JW1859 / Plasmid: pOPINF / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 substr. MG1655 References: UniProt: P76290, 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: 2.42 Å3/Da / Density % sol: 49.14 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Morpheus crystallization screen (Molecular Dimensions) condition E8: 0.3 M diethylene glycol, 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol, 0.1 M ...Details: Morpheus crystallization screen (Molecular Dimensions) condition E8: 0.3 M diethylene glycol, 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol, 0.1 M MOPS/HEPES sodium, pH 7.5, 12.5% w/v PEG1000, 12.5% w/v PEG3350, 12.5% w/v MPD, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2011 / Details: CRL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.73→55.89 Å / Num. all: 52750 / Num. obs: 52750 / % possible obs: 99.9 % / Redundancy: 5 % / Rsym value: 0.056 / Net I/σ(I): 15.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IM8 Resolution: 1.73→55.89 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.096 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 64.75 Å2 / Biso mean: 31.1035 Å2 / Biso min: 13.51 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→55.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.73→1.775 Å / Total num. of bins used: 20
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Refinement TLS params. | T23: 0.0041 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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