+Open data
-Basic information
Entry | Database: PDB / ID: 2fpo | ||||||
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Title | Putative methyltransferase yhhF from Escherichia coli. | ||||||
Components | methylase yhhF | ||||||
Keywords | TRANSFERASE / structural genomics / putative methyltransferase / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information 16S rRNA (guanine966-N2)-methyltransferase / 16S rRNA (guanine(966)-N(2))-methyltransferase activity / rRNA base methylation / nucleic acid binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å | ||||||
Authors | Osipiuk, J. / Kim, Y. / Sanishvili, R. / Skarina, T. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure. Authors: Lesnyak, D.V. / Osipiuk, J. / Skarina, T. / Sergiev, P.V. / Bogdanov, A.A. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Dontsova, O.A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S). THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fpo.cif.gz | 219.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fpo.ent.gz | 184.9 KB | Display | PDB format |
PDBx/mmJSON format | 2fpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fpo_validation.pdf.gz | 484.9 KB | Display | wwPDB validaton report |
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Full document | 2fpo_full_validation.pdf.gz | 503.7 KB | Display | |
Data in XML | 2fpo_validation.xml.gz | 43.5 KB | Display | |
Data in CIF | 2fpo_validation.cif.gz | 61.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/2fpo ftp://data.pdbj.org/pub/pdb/validation_reports/fp/2fpo | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 22181.572 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yhhF / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P0ADX9, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-EDO / | #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: 2.49 Å3/Da / Density % sol: 50.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M sodium tartrate, 20% PEG 3350 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97956 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 25, 2005 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97956 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→38.76 Å / Num. all: 80096 / Num. obs: 80096 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.89 / Num. unique all: 5233 / % possible all: 76.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.05→38.76 Å / Cor.coef. Fo:Fc: 0.957 / SU B: 6.305 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / σ(I): 0 / ESU R: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET.
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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: 33.642 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→38.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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