+
Open data
-
Basic information
Entry | Database: PDB / ID: 5zmp | ||||||
---|---|---|---|---|---|---|---|
Title | The structure of a lysine deacylase | ||||||
![]() | lysine deacylase | ||||||
![]() | HYDROLASE / lysine deacylase | ||||||
Function / homology | Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / hydrolase activity / Acetylpolyamine aminohydrolase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ge, F. | ||||||
![]() | |||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 78.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 56.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 426.5 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g11S S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 34090.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Source details | Protein used in this structure is derived from Tax ID 374982 (Synechococcus sp. PCC 73109). ...Protein used in this structure is derived from Tax ID 374982 (Synechococcus sp. PCC 73109). Reference source is Tax ID 32049 (Synechococcus sp. PCC 7002). Sequences are 100 % matched. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.78 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 1.26 M Sodium phosphate monobasic monohydrate, 0.14 M Potassium phosphate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→50.7 Å / Num. obs: 18344 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.132 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.19→2.25 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1342 / Rpim(I) all: 0.681 / % possible all: 99.8 |
-
Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5G11 Resolution: 2.19→50 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.19→50 Å
| ||||||||||||||||
LS refinement shell | Resolution: 2.19→2.25 Å /
|