+Open data
-Basic information
Entry | Database: PDB / ID: 4z9j | ||||||
---|---|---|---|---|---|---|---|
Title | Apo-Tar from E. coli | ||||||
Components | Methyl-accepting chemotaxis protein II | ||||||
Keywords | PROTEIN BINDING / Bacterial chemotaxis / Aspartate receptor / Aspartate-binding protein | ||||||
Function / homology | Function and homology information detection of chemical stimulus / methyl accepting chemotaxis protein complex / protein histidine kinase binding / positive regulation of post-translational protein modification / cell tip / regulation of chemotaxis / signal complex assembly / cellular response to amino acid stimulus / protein homooligomerization / chemotaxis ...detection of chemical stimulus / methyl accepting chemotaxis protein complex / protein histidine kinase binding / positive regulation of post-translational protein modification / cell tip / regulation of chemotaxis / signal complex assembly / cellular response to amino acid stimulus / protein homooligomerization / chemotaxis / transmembrane signaling receptor activity / signal transduction / protein homodimerization activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Mise, T. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Structural Analysis of the Ligand-Binding Domain of the Aspartate Receptor Tar from Escherichia coli Authors: Mise, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4z9j.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4z9j.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 4z9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/4z9j ftp://data.pdbj.org/pub/pdb/validation_reports/z9/4z9j | HTTPS FTP |
---|
-Related structure data
Related structure data | 4z9hC 4z9iC 2asrS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22283.730 Da / Num. of mol.: 2 / Fragment: UNP residues 26-193 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: tar, cheM / Production host: Escherichia coli (E. coli) / References: UniProt: P07017 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.66 % |
---|---|
Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / Details: NaCl |
-Data collection
Diffraction | Mean temperature: 173 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→53.832 Å / Num. obs: 34426 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.78→1.88 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 6.2 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ASR Resolution: 1.78→53.83 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.41 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.123 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.53 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→53.83 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|