[English] 日本語
![](img/lk-miru.gif)
- PDB-1h6d: Oxidized Precursor Form of Glucose-Fructose Oxidoreductase from Z... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1h6d | ||||||
---|---|---|---|---|---|---|---|
Title | Oxidized Precursor Form of Glucose-Fructose Oxidoreductase from Zymomonas mobilis complexed with glycerol | ||||||
![]() | PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE | ||||||
![]() | PROTEIN TRANSLOCATION / PERIPLASMIC OXIDOREDUCTASE / SIGNAL PEPTIDE / LIGAND BINDING | ||||||
Function / homology | ![]() glucose-fructose oxidoreductase / sorbitol biosynthetic process / glucose-fructose oxidoreductase activity / periplasmic space / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nurizzo, D. / Baker, E.N. | ||||||
![]() | ![]() Title: Crystal Structures of the Precursor Form of Glucose-Fructose Oxidoreductase from Zymomonas Mobilis and its Complexes with Bound Ligands Authors: Nurizzo, D. / Halbig, D. / Sprenger, G. / Baker, E.N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 954.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 794.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3.9 MB | Display | |
Data in XML | ![]() | 211.6 KB | Display | |
Data in CIF | ![]() | 291.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1h6aC ![]() 1h6bC ![]() 1h6cC ![]() 1ofgS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 47342.578 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: NADP, GLYCEROL / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P75002, UniProt: Q07982*PLUS, glucose-fructose oxidoreductase #2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Sequence details | MATURE FORM OF GLUCOSE FRUCTOSE OXIDOREDUC | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6 Details: 12% PEG6000, 550MM AMMONIUM SULFATE, 20% GLYCEROL, pH 6.00 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: DOUBLE FOCUSING MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→15 Å / Num. obs: 317883 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9 |
Reflection shell | *PLUS % possible obs: 99.9 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1OFG Resolution: 2.05→15 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4197810.8 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.0272 Å2 / ksol: 0.396131 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|