[English] 日本語
![](img/lk-miru.gif)
- PDB-4zcl: Crystal Structure of Escherichia coli GTPase BipA/TypA Complexed ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4zcl | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Escherichia coli GTPase BipA/TypA Complexed with GDP | ||||||
![]() | GTP-binding protein TypA/BipA | ||||||
![]() | GTP-binding protein / BipA / GTPase / Nucleotide | ||||||
Function / homology | ![]() guanosine tetraphosphate binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosomal large subunit assembly / ribosome biogenesis / ribosome binding / tRNA binding / rRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding ...guanosine tetraphosphate binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosomal large subunit assembly / ribosome biogenesis / ribosome binding / tRNA binding / rRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fan, H.T. / Hahm, J. / Diggs, S. / Blaha, G. | ||||||
![]() | ![]() Title: Structural and Functional Analysis of BipA, a Regulator of Virulence in Enteropathogenic Escherichia coli. Authors: Fan, H. / Hahm, J. / Diggs, S. / Perry, J.J. / Blaha, G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 449.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 367.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 40.6 KB | Display | |
Data in CIF | ![]() | 54.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zciSC ![]() 4zckC ![]() 4zcmC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 70307.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: typA, bipA, yihK, b3871, JW5571 / Production host: ![]() ![]() #2: Chemical | ChemComp-NCO / #3: Chemical | #4: Chemical | ChemComp-MG / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.61 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100 mM Tris-HCl, 2 % PEG 6000, and 5 mM [Co(NH3)6]Cl3, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 7, 2014 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.06→48.181 Å / Num. obs: 29871 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 72.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 3.06→3.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2 / % possible all: 98.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4ZCI Resolution: 3.06→48.181 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.48 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.06→48.181 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|