[English] 日本語
![](img/lk-miru.gif)
- PDB-4h2w: Crystal structure of engineered Bradyrhizobium japonicum glycine:... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4h2w | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of engineered Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with carrier protein from Agrobacterium tumefaciens and AMP | ||||||
![]() |
| ||||||
![]() | LIGASE / ATP binding / glycine binding / carrier protein / aminoacyl-tRNA synthetase / seryl-tRNA synthetase | ||||||
Function / homology | ![]() : / aminoacyl-tRNA ligase activity / tRNA aminoacylation for protein translation / ligase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Luic, M. / Weygand-Durasevic, I. / Ivic, N. / Mocibob, M. | ||||||
![]() | ![]() Title: Adaptation of aminoacyl-tRNA synthetase catalytic core to carrier protein aminoacylation. Authors: Mocibob, M. / Ivic, N. / Luic, M. / Weygand-Durasevic, I. #1: ![]() Title: Homologs of aminoacyl-tRNA synthetases acylate carrier proteins and provide a link between ribosomal and nonribosomal peptide synthesis Authors: Mocibob, M. / Ivic, N. / Bilokapic, S. / Maier, T. / Luic, M. / Ban, N. / Weygand-Durasevic, I. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 169.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 137.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 45.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4h2sC ![]() 4h2tC ![]() 4h2uC ![]() 4h2vC ![]() 4h2xC ![]() 4h2yC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 38173.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: USDA 110 / Gene: bll0957, Atu2573,AGR_C_4663 / Plasmid: pET28 / Production host: ![]() ![]() References: UniProt: Q89VT8, UniProt: Q7CWR3, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases #2: Protein | Mass: 11165.596 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 6 types, 377 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/5GP.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/PNS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/5GP.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/PNS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-5GP / | #6: Chemical | ChemComp-AMP / | #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | CHAINS A, B ARE CHIMERIC PROTEINS COMPOSED OF UNP RESIDUES Q89VT8 1-220, Q7CWR3 236-246, Q89VT8 232-326 |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.3 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 10% PEG 4000, 10% PEG 8000, 0.17M ammonium acetate, 0.085M trisodium citrate dyhydrate pH 5.6, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 5, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.94→45.755 Å / Num. all: 76863 / Num. obs: 76787 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 33.426 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 24.32 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.58 Å2 / Biso mean: 33.1615 Å2 / Biso min: 7.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→45.755 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27
|