[English] 日本語
![](img/lk-miru.gif)
- PDB-8xaw: Cryo-EM structure of an anti-phage defense complex bound to AMPPN... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8xaw | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of an anti-phage defense complex bound to AMPPNP and DNA at state 1 | ||||||
![]() |
| ||||||
![]() | DNA BINDING PROTEIN / HerA / Helicase DUF4297 / Endonuclease | ||||||
Function / homology | ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / : / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.73 Å | ||||||
![]() | An, Q. / Deng, Z. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: Cryo-EM structure of DUF4297Q53AK55A-HerA-AMPPNP-DNA Authors: An, Q. / Deng, Z. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 156.5 KB | Display | |
Data in CIF | ![]() | 239.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 38205MC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Protein , 2 types, 18 molecules ABCDEFGHIJKLMNOPQR
#1: Protein | Mass: 64870.047 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 46971.949 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-DNA chain , 2 types, 2 molecules ST
#3: DNA chain | Mass: 18035.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#4: DNA chain | Mass: 18333.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 3 types, 12 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ANP.gif)
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: DUF4297-HerA-DNA-state2 / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
---|---|
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-
Processing
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3D reconstruction | Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 365976 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|