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Yorodumi- PDB-7qhv: Crystal structure of the sulfoquinovosyl binding protein SmoF com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qhv | ||||||
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Title | Crystal structure of the sulfoquinovosyl binding protein SmoF complexed with sulfoquinovosyl diacylglycerol | ||||||
Components | Sulfoquinovosyl binding protein | ||||||
Keywords | SUGAR BINDING PROTEIN / agrobacterium / sulfoquinovose / SmoF | ||||||
Function / homology | Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / Chem-CQI / GLYCINE / Maltose-binding periplasmic protein Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Snow, A. / Davies, G.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Curr Res Struct Biol / Year: 2022 Title: The sulfoquinovosyl glycerol binding protein SmoF binds and accommodates plant sulfolipids. Authors: Snow, A.J.D. / Sharma, M. / Lingford, J.P. / Zhang, Y. / Mui, J.W. / Epa, R. / Goddard-Borger, E.D. / Williams, S.J. / Davies, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qhv.cif.gz | 297.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qhv.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7qhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qhv_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7qhv_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7qhv_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 7qhv_validation.cif.gz | 43.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/7qhv ftp://data.pdbj.org/pub/pdb/validation_reports/qh/7qhv | HTTPS FTP |
-Related structure data
Related structure data | 7yzsC 7yzuC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44074.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: SY94_3278 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A083ZKV5 #2: Chemical | #3: Chemical | ChemComp-GLY / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.98 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M L-Na-glutamate, alanine, glycine, lysine hydrochloride, serine, 0.1M TRIS, bicine, 12.5% MPD, PEG1000, PEG3350 |
-Data collection
Diffraction | Mean temperature: 210 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97933 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 17, 2019 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.14→69.59 Å / Num. obs: 42301 / % possible obs: 99.9 % / Redundancy: 4.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.081 / Rrim(I) all: 0.124 / Net I/σ(I): 8.9 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: D_1292119394 Resolution: 2.14→57.995 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.887 / SU B: 6.881 / SU ML: 0.177 / Cross valid method: FREE R-VALUE / ESU R: 0.277 / ESU R Free: 0.221 Details: Hydrogens have been added in their riding positions
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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: 24.287 Å2
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Refinement step | Cycle: LAST / Resolution: 2.14→57.995 Å
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Refine LS restraints |
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LS refinement shell |
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