[English] 日本語
Yorodumi- PDB-8ods: Phosphate-Binding Protein (PstS) from Xanthomonas citri pv. citri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ods | ||||||
---|---|---|---|---|---|---|---|
Title | Phosphate-Binding Protein (PstS) from Xanthomonas citri pv. citri A306 bound to phosphate | ||||||
Components | Phosphate-binding protein PstS | ||||||
Keywords | TRANSPORT PROTEIN / SBP / Pho Regulon / ABC transporter | ||||||
Function / homology | Phosphate ABC transporter, substrate-binding protein PstS / PBP superfamily domain / PBP domain / phosphate ion transmembrane transport / phosphate ion binding / ATP-binding cassette (ABC) transporter complex / Prokaryotic membrane lipoprotein lipid attachment site profile. / PHOSPHATE ION / Phosphate-binding protein PstS Function and homology information | ||||||
Biological species | Xanthomonas citri pv. citri str. 306 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.909 Å | ||||||
Authors | Santos, L.S. / Balan, A. / Guskov, A. | ||||||
Funding support | Brazil, 1items
| ||||||
Citation | Journal: To Be Published Title: Phosphate-Binding Protein (PstS) from Xanthomonas citri pv. citri A306 Authors: Santos, L.S. / Balan, A. / Guskov, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ods.cif.gz | 80.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ods.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 8ods.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ods_validation.pdf.gz | 815.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8ods_full_validation.pdf.gz | 816 KB | Display | |
Data in XML | 8ods_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 8ods_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/8ods ftp://data.pdbj.org/pub/pdb/validation_reports/od/8ods | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36144.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas citri pv. citri str. 306 (bacteria) Strain: A306 / Gene: pstS / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8PM56 |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: 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: 2.2 Å3/Da / Density % sol: 44.29 % |
---|---|
Crystal grow | Temperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris-HCl (pH 8.0), 50 mM KCl, 20% PEG 6000, 20 mg/ml protein |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 3, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873128 Å / Relative weight: 1 |
Reflection | Resolution: 1.909→41.04 Å / Num. obs: 24939 / % possible obs: 97.6 % / Redundancy: 8.6 % / Biso Wilson estimate: 18.53 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.09772 / Rpim(I) all: 0.03365 / Rrim(I) all: 0.1001 / Net I/σ(I): 14.73 |
Reflection shell | Resolution: 1.909→1.977 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 3.01 / Num. unique obs: 2201 / CC1/2: 0.921 / CC star: 0.979 / Rpim(I) all: 0.2064 / Rrim(I) all: 0.4674 / % possible all: 87.58 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.909→41.04 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.882 / SU R Cruickshank DPI: 0.17 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.189 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.157
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.78 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.909→41.04 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.91→1.93 Å
|