[English] 日本語
Yorodumi- PDB-7shj: Crystal structure of Acinetobacter baumannii ZnuA in the metal-fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7shj | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Acinetobacter baumannii ZnuA in the metal-free state | |||||||||
Components | Zinc ABC transporter solute-binding protein | |||||||||
Keywords | METAL BINDING PROTEIN / zinc / solute-binding protein / ABC transporter / host-pathogen / ZnuA | |||||||||
Function / homology | Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / metal ion transport / metal ion binding / Zinc ABC transporter solute-binding protein Function and homology information | |||||||||
Biological species | Acinetobacter baumannii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | |||||||||
Authors | Luo, Z. / McDevitt, C.A. / Kobe, B. | |||||||||
Funding support | Australia, 2items
| |||||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2022 Title: Structural and biochemical characterization of Acinetobacter baumannii ZnuA. Authors: Alquethamy, S. / Ganio, K. / Luo, Z. / Hossain, S.I. / Hayes, A.J. / Ve, T. / Davies, M.R. / Deplazes, E. / Kobe, B. / McDevitt, C.A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7shj.cif.gz | 296.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7shj.ent.gz | 234.2 KB | Display | PDB format |
PDBx/mmJSON format | 7shj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7shj_validation.pdf.gz | 441.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7shj_full_validation.pdf.gz | 446.2 KB | Display | |
Data in XML | 7shj_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 7shj_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/7shj ftp://data.pdbj.org/pub/pdb/validation_reports/sh/7shj | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32033.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: G3N04_06260, G3N12_05260, G3N53_14455, GY141_09205 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6B2IEQ3 #2: Chemical | ChemComp-NA / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.77 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M cirtate pH 7.0, 30% (v/v) polyethylene glycol 6000, and 1 M LiCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→45.55 Å / Num. obs: 27410 / % possible obs: 99.6 % / Redundancy: 2 % / Biso Wilson estimate: 34.29 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.13→2.21 Å / Rmerge(I) obs: 0.51 / Num. unique obs: 2701 / CC1/2: 0.57 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: model generated by alphaFold2 Resolution: 2.13→45.55 Å / SU ML: 0.2779 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.1005 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: 48.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→45.55 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|