[English] 日本語
![](img/lk-miru.gif)
- PDB-8sbn: Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogen... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8sbn | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (P21 Form 1) | |||||||||
![]() | Dephospho-CoA kinase | |||||||||
![]() | TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE | |||||||||
Function / homology | ![]() dephospho-CoA kinase / dephospho-CoA kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (P21 Form 1) Authors: Seibold, S. / Lovell, S. / Liu, L. / Battaile, K.P. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 111.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 84.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 447.4 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 19 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 23850.084 Da / Num. of mol.: 1 / Mutation: G2T, V127I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: coaE, EAE_11320 / Plasmid: KlaeA.00139.a.B1 / Production host: ![]() ![]() | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.47 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Berkeley H6: 20% (w/v) PEG 1500, 12% (w/v) 1,6-hexanediol, 100 mM MES pH5.5, 100 mM CaCl2. 2mM CoA added prior to crystallization but not observed in the electron density. KlaeA.00139.a.B1. ...Details: Berkeley H6: 20% (w/v) PEG 1500, 12% (w/v) 1,6-hexanediol, 100 mM MES pH5.5, 100 mM CaCl2. 2mM CoA added prior to crystallization but not observed in the electron density. KlaeA.00139.a.B1.PW39166 at 24.8 mg/mL. Plate: 13151, well H6 drop 3, Puck: PSL-1415, Cryo: 80% Berkeley H6 + 20% PEG 200 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 14, 2022 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→48.73 Å / Num. obs: 68101 / % possible obs: 98.6 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.018 / Rrim(I) all: 0.046 / Χ2: 0.97 / Net I/σ(I): 15.9 / Num. measured all: 421459 |
Reflection shell | Resolution: 1.15→1.17 Å / % possible obs: 81.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.637 / Num. measured all: 10653 / Num. unique obs: 2750 / CC1/2: 0.774 / Rpim(I) all: 0.362 / Rrim(I) all: 0.738 / Χ2: 1.05 / Net I/σ(I) obs: 1.8 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→30.77 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|