+
Open data
-
Basic information
Entry | Database: PDB / ID: 3asv | ||||||
---|---|---|---|---|---|---|---|
Title | The Closed form of serine dehydrogenase complexed with NADP+ | ||||||
![]() | Short-chain dehydrogenase/reductase SDR | ||||||
![]() | OXIDOREDUCTASE / SDR family / Rossmann fold / short-chain dehydrogenase/reductase / L-allo-threonine dehydrogenase | ||||||
Function / homology | NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PHOSPHATE ION![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamazawa, R. / Nakajima, Y. / Yoshimoto, T. / Ito, K. | ||||||
![]() | ![]() Title: Crystal structure of serine dehydrogenase from Escherichia coli: important role of the C-terminal region for closed-complex formation. Authors: Yamazawa, R. / Nakajima, Y. / Mushiake, K. / Yoshimoto, T. / Ito, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 299.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 244.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 63 KB | Display | |
Data in CIF | ![]() | 82.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3asuSC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 27277.887 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN (ESCHERICHI | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.54 % / Mosaicity: 0.906 ° |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: Na/K phosphate, lithium sulfate, Na acetate buffer, pH 4.5, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 1, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 39711 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.126 / Χ2: 1.154 / Net I/σ(I): 6.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3ASU Resolution: 2.7→20 Å / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 3235134 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: maximum likelihood target using amplitudes Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.1537 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.06 Å2 / Biso mean: 34.253 Å2 / Biso min: 10.32 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.8 Å / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|