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Yorodumi- PDB-5ftw: Crystal structure of glutamate O-methyltransferase in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ftw | ||||||
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Title | Crystal structure of glutamate O-methyltransferase in complex with S- adenosyl-L-homocysteine (SAH) from Bacillus subtilis | ||||||
Components | CHEMOTAXIS PROTEIN METHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / METHYLTRANSFERASE / SAH | ||||||
Function / homology | Function and homology information protein-glutamate O-methyltransferase / protein-glutamate O-methyltransferase activity / chemotaxis Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sharma, R. / Dhindwal, S. / Batra, M. / Aggarwal, M. / Kumar, P. / Tomar, S. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2016 Title: Crystal Structure of Pentapeptide-Independent Chemotaxis Receptor Methyltransferase (Cher) Reveals Idiosyncratic Structural Determinants for Receptor Recognition. Authors: Batra, M. / Sharma, R. / Malik, A. / Dhindwal, S. / Kumar, P. / Tomar, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ftw.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ftw.ent.gz | 56.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ftw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ftw_validation.pdf.gz | 741.3 KB | Display | wwPDB validaton report |
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Full document | 5ftw_full_validation.pdf.gz | 748 KB | Display | |
Data in XML | 5ftw_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 5ftw_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/5ftw ftp://data.pdbj.org/pub/pdb/validation_reports/ft/5ftw | HTTPS FTP |
-Related structure data
Related structure data | 1bc5S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29994.453 Da / Num. of mol.: 1 / Fragment: SAH BINDING DOMAIN, UNP RESIDUES 1-256 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Description: MTCC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA References: UniProt: P31105, protein-glutamate O-methyltransferase |
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-Non-polymers , 5 types, 303 molecules
#2: Chemical | ChemComp-SAH / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-TRS / | #5: Chemical | #6: 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: 2 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | Details: 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE TRIHYDRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 30, 2013 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→41.58 Å / Num. obs: 23011 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.79→1.89 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.3 / % possible all: 83.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BC5 Resolution: 1.8→36.46 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.568 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 17.554 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→36.46 Å
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Refine LS restraints |
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