[English] 日本語
![](img/lk-miru.gif)
- PDB-3du1: The 2.0 Angstrom Resolution Crystal Structure of HetL, a Pentapep... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3du1 | ||||||
---|---|---|---|---|---|---|---|
Title | The 2.0 Angstrom Resolution Crystal Structure of HetL, a Pentapeptide Repeat Protein involved in Heterocyst Differentiation Regulation from the Cyanobacterium Nostoc sp. Strain PCC 7120 | ||||||
![]() | All3740 protein | ||||||
![]() | STRUCTURAL PROTEIN / Right-handed Beta Helix / Repeated Five Residue Fold / Pentapeptide Repeat Protein | ||||||
Function / homology | Pentapeptide repeats (8 copies) / E3 ubiquitin-protein ligase SopA / Pentapeptide repeat / Pectate Lyase C-like / 3 Solenoid / Mainly Beta / All3740 protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Kennedy, M.A. / Ni, S. / Sheldrick, G.M. | ||||||
![]() | ![]() Title: The 2A resolution crystal structure of HetL, a pentapeptide repeat protein involved in regulation of heterocyst differentiation in the cyanobacterium Nostoc sp. strain PCC 7120 Authors: Ni, S. / Sheldrick, G.M. / Benning, M.M. / Kennedy, M.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 62.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 45.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 415.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 415.8 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 27778.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The protein adopts the repeated five residue (Rfr) fold comprised of a right-handed quadrilateral beta-helix Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.81 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, 0.7M sodium phosphate monobasic, 0.7M potassium phosphate monobasic, 12.5% glycerol, protein concentration 7.5 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Feb 13, 2008 / Details: mirrors |
Radiation | Monochromator: graded thin film multilayer mirror Bragg Diffraction Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→68.84 Å / Num. all: 32008 / Num. obs: 28767 / % possible obs: 89.9 % / Observed criterion σ(I): 3 / Redundancy: 38.58 % / Rsym value: 0.041 / Net I/σ(I): 61.22 |
Reflection shell | Resolution: 1.77→1.87 Å / Redundancy: 38.58 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.63 / Rsym value: 0.3 / % possible all: 58.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: sulfur anomalous scattering / Resolution: 2→28.41 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.582 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.67 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→28.41 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
|