[English] 日本語
![](img/lk-miru.gif)
- PDB-7naa: Crystal structure of Mycobacterium tuberculosis H37Rv PknF kinase... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7naa | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium tuberculosis H37Rv PknF kinase domain | |||||||||
![]() | Non-specific serine/threonine protein kinase | |||||||||
![]() | TRANSFERASE / pknF / Mtb / Structural Genomics / PSI-Biology / Protein Structure Initiative / Structural Genomics Consortium / SGC / ANTIMICROBIAL PROTEIN | |||||||||
Function / homology | ![]() protein serine/threonine kinase activity => GO:0004674 / membrane => GO:0016020 / non-specific serine/threonine protein kinase / protein serine kinase activity / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Oliveira, A.A. / Cabarca, S. / dos Reis, C.V. / Takarada, J.E. / Counago, R.M. / Balan, A. / Structural Genomics Consortium (SGC) | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structure of the Mycobacterium tuberculosis c PknF and conformational changes induced in forkhead-associated regulatory domains. Authors: Cabarca, S. / Frazao de Souza, M. / Albert de Oliveira, A. / Vignoli Muniz, G.S. / Lamy, M.T. / Vinicius Dos Reis, C. / Takarada, J. / Effer, B. / Souza, L.S. / Iriarte de la Torre, L. / ...Authors: Cabarca, S. / Frazao de Souza, M. / Albert de Oliveira, A. / Vignoli Muniz, G.S. / Lamy, M.T. / Vinicius Dos Reis, C. / Takarada, J. / Effer, B. / Souza, L.S. / Iriarte de la Torre, L. / Counago, R. / Pinto Oliveira, C.L. / Balan, A. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 362.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 296.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 46.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5m06S S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
|
-
Components
#1: Protein | Mass: 30371.281 Da / Num. of mol.: 4 / Fragment: Protein kinase domain, residues 1-278 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: pknF_1, pknF, pknF_2, C0094_09540, DSI38_08510, E5M05_19500, E5M52_18375, E5M78_18220, ERS007741_01296, ERS013471_03424, ERS027661_00065, ERS094182_03016, F6W99_00312, FRD82_04005, GCL30_17545, SAMEA2683035_01332 Plasmid: pOP5GT / Details (production host): gst tag / Production host: ![]() ![]() References: UniProt: A0A045H1A5, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-V17 / ( #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.03 % / Description: Orthorhombic |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG 4000, Citrate buffer, Ammonium acetate pH 5.5, 10 mM Ikk16 Temp details: 18 |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→39.9 Å / Num. obs: 34601 / % possible obs: 99.41 % / Redundancy: 5.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.065 / Rrim(I) all: 0.159 / Net I/σ(I): 11.14 |
Reflection shell | Resolution: 2.75→2.84 Å / Rmerge(I) obs: 1.57 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 3428 / CC1/2: 0.6 / Rpim(I) all: 0.76 / Rrim(I) all: 1.76 / % possible all: 98.93 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5m06 Resolution: 2.75→39.9 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.891 / SU B: 36.199 / SU ML: 0.33 / Cross valid method: FREE R-VALUE / ESU R: 0.827 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 64.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.75→39.9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|