[English] 日本語
![](img/lk-miru.gif)
- PDB-2hz8: QM/MM structure refined from NMR-structure of a single chain diir... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2hz8 | ||||||
---|---|---|---|---|---|---|---|
Title | QM/MM structure refined from NMR-structure of a single chain diiron protein | ||||||
![]() | De novo designed diiron protein | ||||||
![]() | DE NOVO PROTEIN / four-helix bundle | ||||||
Function / homology | IL-4 antagonist (De novo design) like domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / 1. Step: Classical Molecular dynamics simulation starting from NMR-structure, using non-bonded model for metal-site. 2. step: QM, MM MD for relaxation of local frustrations at the metal site. | ||||||
![]() | Calhoun, J.R. / Liu, W. / Spiegel, K. / Dal Peraro, M. / Klein, M.L. / Wand, A.J. / DeGrado, W.F. | ||||||
![]() | ![]() Title: Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement. Authors: Calhoun, J.R. / Liu, W. / Spiegel, K. / Dal Peraro, M. / Klein, M.L. / Valentine, K.G. / Wand, A.J. / Degrado, W.F. #1: Journal: J.Mol.Biol. / Year: 2003 Title: Computational design and characterization of a monomeric helical dinuclear metalloprotein. Authors: Calhoun, J.R. / Kono, H. / Lahr, S. / Wang, W. / DeGrado, W.F. / Saven, J.G. #2: Journal: Biopolymers / Year: 2005 Title: Artificial diiron proteins: from structure to function. Authors: Calhoun, J.R. / Nastri, F. / Magloi, O. / Pavone, V. / Lombardi, A. / DeGrado, W.F. | ||||||
History |
| ||||||
Remark 999 | Sequence No suitable database references were found at time of processing |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 50.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 36.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 296.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 296.3 KB | Display | |
Data in XML | ![]() | 3.5 KB | Display | |
Data in CIF | ![]() | 4.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-
Components
#1: Protein | Mass: 13516.417 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||||||
NMR details | Text: The structure was first determined using triple-resonance spectrscopy. The structure was then further refined using classical MD followed by 5 ps of Car Parrinello hybrid QM/MM dynamics. |
-
Sample preparation
Details |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample conditions | Ionic strength: 10 mM NaCl / pH: 6.0 / Pressure: ambient / Temperature: 308 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
|
-
Processing
NMR software |
|
---|