[English] 日本語

- PDB-2v4y: THE STRUCTURE OF E. COLI UMP KINASE IN COMPLEX WITH ITS ALLOSTERI... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2v4y | ||||||
---|---|---|---|---|---|---|---|
Title | THE STRUCTURE OF E. COLI UMP KINASE IN COMPLEX WITH ITS ALLOSTERIC REGULATOR GTP | ||||||
![]() | URIDYLATE KINASE | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Meyer, P. / Evrin, C. / Briozzo, P. / Joly, N. / Barzu, O. / Gilles, A.M. | ||||||
![]() | ![]() Title: Structural and Functional Characterization of Escherichia Coli Ump Kinase in Complex with its Allosteric Regulator GTP. Authors: Meyer, P. / Evrin, C. / Briozzo, P. / Joly, N. / Barzu, O. / Gilles, A.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 272.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 230.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3.1 MB | Display | |
Data in XML | ![]() | 57.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bnfS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-
Components
#1: Protein | Mass: 25999.277 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GTP / ![]() #3: Water | ChemComp-HOH / | ![]() Compound details | ENGINEERED RESIDUE IN CHAIN A, ASP 159 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 159 TO ASN ...ENGINEERED | Nonpolymer details | GUANOSINE-5'-TRIPHOSPHATE (GTP): IN A1243, B1243, C1243, D1243, E1243, F1243 ONLY THE PHOSPHATE ...GUANOSINE-5'-TRIPHOSPHA | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.5 % / Description: NONE |
---|---|
Crystal grow![]() | Details: 43% PEG 400, 100 MM SODIUM ACETATE, PH 4.6, 22.5 MM GTP, 100 MM NACL. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→49.15 Å / Num. obs: 34062 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.8→2.88 Å / Redundancy: 7 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2BNF Resolution: 2.8→49.038 Å / SU ML: 0.43 / σ(F): 1.36 / Phase error: 24.01 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.97 Å2 / ksol: 0.348 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→49.038 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|