[English] 日本語
![](img/lk-miru.gif)
- PDB-2nxi: Structural and mechanistic changes along an engineered path from ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2nxi | ||||||
---|---|---|---|---|---|---|---|
Title | Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase. | ||||||
![]() | 2-dehydro-3-deoxyphosphooctonate aldolase | ||||||
![]() | TRANSFERASE / KDO / KDO8P / KDO8PS / PEP / A5P | ||||||
Function / homology | ![]() monosaccharide biosynthetic process / 3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kona, F. / Xu, X. / Martin, P. / Kuzmic, P. / Gatti, D.L. | ||||||
![]() | ![]() Title: Structural and mechanistic changes along an engineered path from metallo to nonmetallo 3-deoxy-D-manno-octulosonate 8-phosphate synthases Authors: Kona, F. / Xu, X. / Martin, P. / Kuzmic, P. / Gatti, D.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 626.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 515.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 578.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 671.5 KB | Display | |
Data in XML | ![]() | 132.3 KB | Display | |
Data in CIF | ![]() | 174.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ef9C ![]() 2nwrC ![]() 2nwsC ![]() 2nx1C ![]() 2nx3C ![]() 2nxgC ![]() 2nxhC ![]() 1fwnS ![]() 2nxk C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 29362.830 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O66496, 3-deoxy-8-phosphooctulonate synthase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-PEP / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.56 % |
---|
-Data collection
Diffraction source | Source: ![]() |
---|---|
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. all: 161988 / Num. obs: 123597 / % possible obs: 76.3 % / Observed criterion σ(F): 4.4 / Observed criterion σ(I): 2.1 / Redundancy: 3.3 % / Biso Wilson estimate: 3.6 Å2 / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / Net I/σ(I): 8.3 |
-
Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1FWN Resolution: 2.3→25 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 653648.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.4769 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|