+
Open data
-
Basic information
Entry | Database: PDB / ID: 1i5d | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF CHEA DOMAIN P4 IN COMPLEX WITH TNP-ATP | ||||||
![]() | CHEMOTAXIS PROTEIN CHEA | ||||||
![]() | SIGNALING PROTEIN / TRANSFERASE / beta-alpha sandwich | ||||||
Function / homology | ![]() histidine kinase / phosphorelay sensor kinase activity / chemotaxis / protein domain specific binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bilwes, A.M. / Quezada, C.M. / Croal, L.R. / Crane, B.R. / Simon, M.I. | ||||||
![]() | ![]() Title: Nucleotide binding by the histidine kinase CheA. Authors: Bilwes, A.M. / Quezada, C.M. / Croal, L.R. / Crane, B.R. / Simon, M.I. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 54.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 38.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1i58C ![]() 1i59C ![]() 1i5aC ![]() 1i5bC ![]() 1i5cC ![]() 1b3qS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 21426.852 Da / Num. of mol.: 1 / Fragment: DOMAIN P4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q56310, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-128 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.6 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: sodium acetate 0.1 M Ammonium sulfate 1.9 M, pH 4.7. VAPOR DIFFUSION, HANGING DROP at 298 K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / PH range low: 4.9 / PH range high: 4.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 17, 1999 |
Radiation | Monochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. all: 7933 / Num. obs: 7933 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 1 % / Biso Wilson estimate: 85.6 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.9→3.04 Å / Redundancy: 1 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 8 / % possible all: 99 |
Reflection | *PLUS % possible obs: 99 % |
Reflection shell | *PLUS % possible obs: 99 % / Mean I/σ(I) obs: 8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1B3Q Resolution: 2.9→27.89 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 92361613.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 103.9 Å2 / ksol: 0.337 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.9 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→27.89 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3 Å / Rfactor Rfree error: 0.097 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5.4 % / Rfactor obs: 0.25 / Rfactor Rfree: 0.308 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 89.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.365 / % reflection Rfree: 4.2 % / Rfactor Rwork: 0.394 |