+Open data
-Basic information
Entry | Database: PDB / ID: 7xg7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of PstS protein from cyanophage Syn19 | ||||||
Components | Phosphate transporter subunit | ||||||
Keywords | TRANSPORT PROTEIN / phosphate binding protein / cyanobacteria / cyanophage | ||||||
Function / homology | Phosphate ABC transporter, substrate-binding protein PstS / PBP superfamily domain / PBP domain / phosphate ion transmembrane transport / phosphate ion binding / PHOSPHATE ION / Phosphate transporter subunit Function and homology information | ||||||
Biological species | Synechococcus phage Syn19 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Cai, K. / Jiang, Y.L. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Environ.Microbiol. / Year: 2022 Title: Biochemical and structural characterization of the cyanophage-encoded phosphate-binding protein: implications for enhanced phosphate uptake of infected cyanobacteria Authors: Zhao, F. / Lin, X. / Cai, K. / Jiang, Y. / Ni, T. / Chen, Y. / Feng, J. / Dang, S. / Zhou, C.Z. / Zeng, Q. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7xg7.cif.gz | 130.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7xg7.ent.gz | 99.8 KB | Display | PDB format |
PDBx/mmJSON format | 7xg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xg7_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7xg7_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7xg7_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 7xg7_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/7xg7 ftp://data.pdbj.org/pub/pdb/validation_reports/xg/7xg7 | HTTPS FTP |
-Related structure data
Related structure data | 7xg8C 2abhS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34119.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus phage Syn19 (virus) / Gene: pstS, Syn19_159 / Production host: Escherichia coli (E. coli) / References: UniProt: E3SQC4 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.15 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 18% (w/v) polyethylene glycol 3350, 0.2 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 79022 / % possible obs: 98.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 14.247 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.658 / Num. unique obs: 7809 / Rsym value: 0.413 / % possible all: 98.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2abh Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.829 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 137.94 Å2 / Biso mean: 21.122 Å2 / Biso min: 6.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.743 Å / Rfactor Rfree error: 0
|