+
Open data
-
Basic information
Entry | Database: PDB / ID: 7zhd | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of CtaZ in complex with Closthioamide | ||||||
![]() | Transcription activator effector binding | ||||||
![]() | LIPID BINDING PROTEIN / GYRASE-LIKE DOMAIN / RECEPTOR / SIDEROPHORE / SELF PROTECTION / ANTIBIOTIC RESISTANCE / DRUG BINDING | ||||||
Function / homology | Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / GyrI-like small molecule binding domain / GyrI-like small molecule binding domain / Regulatory factor, effector binding domain superfamily / Chem-IQ4 / Transcription activator effector binding![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gude, F. / Molloy, E.M. / Horch, T. / Dell, M. / Dunbar, K.L. / Krabbe, J. / Groll, M. / Hertweck, C. | ||||||
Funding support | European Union, 1items
| ||||||
![]() | ![]() Title: A Specialized Polythioamide-Binding Protein Confers Antibiotic Self-Resistance in Anaerobic Bacteria. Authors: Gude, F. / Molloy, E.M. / Horch, T. / Dell, M. / Dunbar, K.L. / Krabbe, J. / Groll, M. / Hertweck, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 80.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 58.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 663.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 664.7 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zheC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17447.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Ccel_3263 / Plasmid: pET28a / Production host: ![]() ![]() |
---|
-Non-polymers , 5 types, 70 molecules ![](data/chem/img/IQ4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-IQ4 / ~{ | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.17 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM Na-cacodylate, 200 mM ZnAc2, 18% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 22520 / % possible obs: 97.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.65→1.75 Å / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3648 / % possible all: 99.3 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.09 Å2 / Biso mean: 35.699 Å2 / Biso min: 22.25 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 33.0722 Å / Origin y: 38.5759 Å / Origin z: 30.2599 Å
|