[English] 日本語
Yorodumi- PDB-2nuu: Regulating the Escherichia coli ammonia channel: the crystal stru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nuu | ||||||
---|---|---|---|---|---|---|---|
Title | Regulating the Escherichia coli ammonia channel: the crystal structure of the AmtB-GlnK complex | ||||||
Components |
| ||||||
Keywords | TRANSPORT PROTEIN/SIGNALING PROTEIN / Membrane protein complex / nitrogen regulation / ammonia transport / TRANSPORT PROTEIN-SIGNALING PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of nitrogen utilization / ammonium transmembrane transport / ammonium channel activity / regulation of nitrogen utilization / enzyme regulator activity / carbon dioxide transport / ATP binding / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Conroy, M.J. / Durand, A. / Lupo, D. / Li, X.-D. / Bullough, P.A. / Winkler, F.K. / Merrick, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: The crystal structure of the Escherichia coli AmtB-GlnK complex reveals how GlnK regulates the ammonia channel Authors: Conroy, M.J. / Durand, A. / Lupo, D. / Li, X.-D. / Bullough, P.A. / Winkler, F.K. / Merrick, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2nuu.cif.gz | 582.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2nuu.ent.gz | 479.3 KB | Display | PDB format |
PDBx/mmJSON format | 2nuu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nuu_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2nuu_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 2nuu_validation.xml.gz | 106.4 KB | Display | |
Data in CIF | 2nuu_validation.cif.gz | 147.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/2nuu ftp://data.pdbj.org/pub/pdb/validation_reports/nu/2nuu | HTTPS FTP |
-Related structure data
Related structure data | 1u7gS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 43397.699 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: GT1000 / Gene: amtB / Plasmid: pAD2 / Production host: Escherichia coli (E. coli) / Strain (production host): GT1000 / References: UniProt: P69681 #2: Protein | Mass: 12276.192 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: GT1000 / Gene: glnK / Plasmid: pAD2 / Production host: Escherichia coli (E. coli) / Strain (production host): GT1000 / References: UniProt: P0AC55 #3: Chemical | ChemComp-ADP / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.45 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 65% MPD, 100mM Tris pH8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97972 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 14, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97972 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 105009 / Redundancy: 4.17 % / Rsym value: 0.0989 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 4.21 % / Mean I/σ(I) obs: 3 / Rsym value: 0.536 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB code 1U7G Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.909 / SU B: 21.864 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 1.121 / ESU R Free: 0.312 / 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: 29.201 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
|