[English] 日本語
Yorodumi- PDB-3k7d: C-terminal (adenylylation) domain of E.coli Glutamine Synthetase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k7d | ||||||
---|---|---|---|---|---|---|---|
Title | C-terminal (adenylylation) domain of E.coli Glutamine Synthetase Adenylyltransferase | ||||||
Components | Glutamate-ammonia-ligase adenylyltransferase | ||||||
Keywords | TRANSFERASE / nucleotidyl transferase domain / ATP-binding / Nucleotide-binding / Nucleotidyltransferase | ||||||
Function / homology | Function and homology information [glutamine synthetase] adenylyltransferase / [glutamine synthetase]-adenylyl-L-tyrosine phosphorylase / regulation of glutamine family amino acid metabolic process / [glutamate-ammonia-ligase] adenylyltransferase activity / [glutamine synthetase]-adenylyl-L-tyrosine phosphorylase activity / metabolic process / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Xu, Y. / Carr, P.D. / Vasudevan, S.G. / Ollis, D.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Structure of the Adenylylation Domain of E. coli Glutamine Synthetase Adenylyl Transferase: Evidence for Gene Duplication and Evolution of a New Active Site. Authors: Xu, Y. / Carr, P.D. / Vasudevan, S.G. / Ollis, D.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3k7d.cif.gz | 213.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3k7d.ent.gz | 170.9 KB | Display | PDB format |
PDBx/mmJSON format | 3k7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/3k7d ftp://data.pdbj.org/pub/pdb/validation_reports/k7/3k7d | HTTPS FTP |
---|
-Related structure data
Related structure data | 1v4aS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 57228.953 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 449-946) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Gene: b3053, glnE, JW3025 / Plasmid: pAT-C505 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: P30870, [glutamine synthetase] adenylyltransferase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.01 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2M ammonium sulfate, 0.1M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 10, 2004 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 51021 / Num. obs: 49185 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.2 / % possible all: 93.8 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1v4a Resolution: 2.4→47.13 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0.32 / SU B: 14.109 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.363 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.868 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→47.13 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|