+
Open data
-
Basic information
Entry | Database: PDB / ID: 2x86 | ||||||
---|---|---|---|---|---|---|---|
Title | AGME bound to ADP-B-mannose | ||||||
![]() | ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE | ||||||
![]() | ISOMERASE / LIPOPOLYSACCHARIDE BIOSYNTHESIS / CARBOHYDRATE METABOLISM / STRESS RESPONSE | ||||||
Function / homology | ![]() ADP-glyceromanno-heptose 6-epimerase / ADP-glyceromanno-heptose 6-epimerase activity / ADP-L-glycero-beta-D-manno-heptose biosynthetic process / lipopolysaccharide core region biosynthetic process / NADP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kowatz, T. / Morrison, J.P. / Tanner, M.E. / Naismith, J.H. | ||||||
![]() | ![]() Title: The Crystal Structure of the Y140F Mutant of Adp-L-Glycero-D-Manno-Heptose 6-Epimerase Bound to Adp-Beta-D-Mannose Suggests a One Base Mechanism. Authors: Kowatz, T. / Morrison, J.P. / Tanner, M.E. / Naismith, J.H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 1017.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 14.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 14.2 MB | Display | |
Data in XML | ![]() | 225.6 KB | Display | |
Data in CIF | ![]() | 289 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2x6tC ![]() 1eq2S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 39891.512 Da / Num. of mol.: 20 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P67911, ADP-glyceromanno-heptose 6-epimerase #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-ADP / #4: Sugar | ChemComp-BMA / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN B, TYR 140 TO PHE ...ENGINEERED | Sequence details | HIS TAG AT N-TERMINUS, Y140F MUTATION | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.75 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU CCD RIGAKU / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→33 Å / Num. obs: 197672 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.8 / % possible all: 92 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EQ2 Resolution: 2.8→35.05 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.902 / SU B: 32.587 / SU ML: 0.303 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.417 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.715 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→35.05 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|