+Open data
-Basic information
Entry | Database: PDB / ID: 4qnx | ||||||
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Title | Crystal structure of apo-CmoB | ||||||
Components | tRNA (mo5U34)-methyltransferase | ||||||
Keywords | TRANSFERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Rossmann Fold | ||||||
Function / homology | Function and homology information tRNA wobble uridine modification / transferase activity, transferring alkyl or aryl (other than methyl) groups / Transferases; Transferring alkyl or aryl groups, other than methyl groups / protein homotetramerization / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.619 Å | ||||||
Authors | Kim, J. / Toro, R. / Bhosle, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2015 Title: Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification. Authors: Kim, J. / Xiao, H. / Koh, J. / Wang, Y. / Bonanno, J.B. / Thomas, K. / Babbitt, P.C. / Brown, S. / 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 | 4qnx.cif.gz | 140.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qnx.ent.gz | 111.3 KB | Display | PDB format |
PDBx/mmJSON format | 4qnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qnx_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 4qnx_full_validation.pdf.gz | 455 KB | Display | |
Data in XML | 4qnx_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 4qnx_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/4qnx ftp://data.pdbj.org/pub/pdb/validation_reports/qn/4qnx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37052.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1871, cmoB, JW1860, yecP / Plasmid: LIC pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: P76291, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | ChemComp-SO4 / #3: 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: 3.51 Å3/Da / Density % sol: 64.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.26M ammonium sulfate, and 100mM HEPES/NaOH pH 7.5, 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 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2010 |
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: 2.63→50 Å / Num. all: 30537 / Num. obs: 30190 / % possible obs: 98.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 18.14 |
Reflection shell | Resolution: 2.63→2.68 Å / Redundancy: 5 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.619→47.537 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 27.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.619→47.537 Å
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Refine LS restraints |
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LS refinement shell |
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