[English] 日本語
![](img/lk-miru.gif)
- PDB-7jjb: Crystal structure of Zn(II)-bound ZinT-like domain of Streptococc... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7jjb | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Zn(II)-bound ZinT-like domain of Streptococcus pneumoniae AdcA | |||||||||||||||
![]() | Zinc-binding lipoprotein AdcA | |||||||||||||||
![]() | METAL BINDING PROTEIN / AdcA / ZinT / SBP / ATP-binding cassette transporter / Zn acquisition | |||||||||||||||
Function / homology | ![]() zinc ion transport / establishment of competence for transformation / cell adhesion / zinc ion binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Luo, Z. / More, J.R. / Kobe, B. / McDevitt, C.A. | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() Title: A Trap-Door Mechanism for Zinc Acquisition by Streptococcus pneumoniae AdcA. Authors: Luo, Z. / Morey, J.R. / Deplazes, E. / Motygullina, A. / Tan, A. / Ganio, K. / Neville, S.L. / Eleftheriadis, N. / Isselstein, M. / Pederick, V.G. / Paton, J.C. / Cordes, T. / Harmer, J.R. / ...Authors: Luo, Z. / Morey, J.R. / Deplazes, E. / Motygullina, A. / Tan, A. / Ganio, K. / Neville, S.L. / Eleftheriadis, N. / Isselstein, M. / Pederick, V.G. / Paton, J.C. / Cordes, T. / Harmer, J.R. / Kobe, B. / McDevitt, C.A. | |||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 155.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 100.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jj8C ![]() 7jj9C ![]() 7jjaC ![]() 1oekS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 20906.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-255 / R6 / Gene: adcA, spr1975 / Production host: ![]() ![]() | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.79 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1 M sodium acetate, pH 4.5, 30 % (w/v) PEG MME 5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→19.72 Å / Num. obs: 79405 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 9.30931181088 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.03 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.1→1.14 Å / Rmerge(I) obs: 0.29 / Num. unique obs: 7855 / CC1/2: 0.8 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1OEK Resolution: 1.1→19.72 Å / SU ML: 0.0905886820257 / Cross valid method: FREE R-VALUE / σ(F): 1.33414552556 / Phase error: 14.4594981077 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: 16.3663010563 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→19.72 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|