[English] 日本語
![](img/lk-miru.gif)
- PDB-7m97: Crystal structure of the bromodomain from Plasmodium falciparum b... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7m97 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the bromodomain from Plasmodium falciparum bromodomain protein 1 | ||||||
![]() | Bromodomain protein 1 | ||||||
![]() | NUCLEAR PROTEIN / bromodomain | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Glass, K.C. | ||||||
![]() | ![]() Title: Crystal structure of the bromodomain from Plasmodium falciparum bromodomain protein 1 Authors: Alkrimi, S. / Phillips, M. / Nix, J.C. / Glass, K.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 77.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 51 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 422.8 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 10.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ulcS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 15037.358 Da / Num. of mol.: 1 / Mutation: E458S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: isolate 3D7 / Gene: PF3D7_1033700 / Production host: ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.65 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.3 M lithium sulfate, 0.1 M tris, pH 8.5, 38% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Jul 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2→35.84 Å / Num. obs: 12597 / % possible obs: 99.63 % / Redundancy: 2 % / Biso Wilson estimate: 29.39 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02602 / Rpim(I) all: 0.02602 / Rrim(I) all: 0.0368 / Net I/σ(I): 19.24 |
Reflection shell | Resolution: 2→2.072 Å / Rmerge(I) obs: 0.2672 / Mean I/σ(I) obs: 2.93 / Num. unique obs: 1203 / CC1/2: 0.93 / CC star: 0.982 / Rpim(I) all: 0.2672 / Rrim(I) all: 0.3779 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5ulc Resolution: 2→35.84 Å / SU ML: 0.1874 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8313 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.01 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→35.84 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 34.9863714822 Å / Origin y: 20.3868843445 Å / Origin z: 40.5860127109 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |