+
Open data
-
Basic information
Entry | Database: PDB / ID: 1f1e | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE HISTONE FROM METHANOPYRUS KANDLERI | ||||||
![]() | HISTONE FOLD PROTEIN | ||||||
![]() | DNA BINDING PROTEIN / Archaeal Histone Protein | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fahrner, R.L. / Cascio, D. / Lake, J.A. / Slesarev, A. | ||||||
![]() | ![]() Title: An ancestral nuclear protein assembly: crystal structure of the Methanopyrus kandleri histone. Authors: Fahrner, R.L. / Cascio, D. / Lake, J.A. / Slesarev, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 79.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 63.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 369 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 374 KB | Display | |
Data in XML | ![]() | 5.3 KB | Display | |
Data in CIF | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
| |||||||||
Details | The biological assembly is a monomer and a dimer created by the crystallographic two fold. |
-
Components
#1: Protein | Mass: 17214.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Protein: 18mg/ml HMK, 1M NaCl, 50mM Tris pH 8.5, 50mM BME, Well: 400mM NaCl, 50mM Tris pH 8.5, 50mM BME, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 12, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.78 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→30 Å / Num. all: 34781 / Num. obs: 31694 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.37→1.39 Å / Redundancy: 4 % / Rmerge(I) obs: 0.475 / Num. unique all: 1709 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 30 Å |
Reflection shell | *PLUS % possible obs: 99.9 % |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.37→30 Å / Num. parameters: 12837 / Num. restraintsaints: 16871 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER Details: Anisotropic scaling applied by the method of Parkin, Moezzi, and Hope, J. Appl.Cryst. 28(1995)53-56.
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: Moews & Kretsinger, J. Mol. Biol. 91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 33 / Occupancy sum hydrogen: 1100.02 / Occupancy sum non hydrogen: 1292.63 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→30 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 8.5 % / Rfactor obs: 0.163 / Rfactor Rfree: 0.208 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|