[English] 日本語
Yorodumi- PDB-8s5b: Crystal structure of the sulfoquinovosyl binding protein (SmoF) f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8s5b | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the sulfoquinovosyl binding protein (SmoF) from A. tumefaciens sulfo-SMO pathway in complex with SQOctyl ligand | |||||||||
Components | Sulfoquinovosyl glycerol-binding protein SmoF | |||||||||
Keywords | SUGAR BINDING PROTEIN / agrobacterium tumefaciens / sulfoquinovose / sulfosugar / solute binding protein / sulfoglycolysis / sulfo-SMO pathway | |||||||||
Function / homology | carbohydrate transport / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / : / Sulfoquinovosyl glycerol-binding protein SmoF Function and homology information | |||||||||
Biological species | Agrobacterium tumefaciens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Snow, A.J.D. / Sharma, M. / Davies, G.J. | |||||||||
Funding support | United Kingdom, 2items
| |||||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2024 Title: Capture-and-release of a sulfoquinovose-binding protein on sulfoquinovose-modified agarose. Authors: Arumapperuma, T. / Snow, A.J.D. / Lee, M. / Sharma, M. / Zhang, Y. / Lingford, J.P. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8s5b.cif.gz | 157.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8s5b.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8s5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/8s5b ftp://data.pdbj.org/pub/pdb/validation_reports/s5/8s5b | 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: 44074.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: smoF, Atu3282 / Production host: Escherichia coli (E. coli) / References: UniProt: A9CEY9 |
---|---|
#2: Chemical | ChemComp-A1H5E / [( Mass: 356.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O8S / Feature type: SUBJECT OF INVESTIGATION |
#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: 2.15 Å3/Da / Density % sol: 42.78 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 200 mM calcium acetate, 100 mM Bis-TRIS pH 6.5, 25% w/v PEG 2000 MME, 1:1 protein:mother liquor ratio with SmoF at 50mg/ml in 50mM TRIS, 300mM NaCl pH 7.5 |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2019 | |||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.8→56.147 Å / Num. obs: 36036 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.965 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.065 / Rrim(I) all: 0.134 / Net I/σ(I): 10.1 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→56.147 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.9 / SU B: 4 / SU ML: 0.123 / Cross valid method: FREE R-VALUE / ESU R: 0.157 / ESU R Free: 0.15 Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.01 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→56.147 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|