+Open data
-Basic information
Entry | Database: PDB / ID: 7yaq | ||||||
---|---|---|---|---|---|---|---|
Title | Phloem lectin (PP2)C34S mutant | ||||||
Components | 17 kDa phloem lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / Phloem lectin / chitin-binding lectin | ||||||
Function / homology | : / Phloem protein 2-like / Phloem protein 2 / carbohydrate binding / 17 kDa phloem lectin Function and homology information | ||||||
Biological species | Cucumis sativus (cucumber) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.853 Å | ||||||
Authors | Sivaji, N. / Bobbili, K.B. / Priya, B. / Suguna, K. / Surolia, A. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: Structure / Year: 2023 Title: Structure and interactions of the phloem lectin (phloem protein 2) Cus17 from Cucumis sativus. Authors: Bobbili, K.B. / Sivaji, N. / Priya, B. / Suguna, K. / Surolia, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7yaq.cif.gz | 46.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7yaq.ent.gz | 30.7 KB | Display | PDB format |
PDBx/mmJSON format | 7yaq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yaq_validation.pdf.gz | 423.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7yaq_full_validation.pdf.gz | 423.3 KB | Display | |
Data in XML | 7yaq_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 7yaq_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/7yaq ftp://data.pdbj.org/pub/pdb/validation_reports/ya/7yaq | HTTPS FTP |
-Related structure data
Related structure data | 7vubS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 17623.807 Da / Num. of mol.: 1 / Mutation: C34S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cucumis sativus (cucumber) / Gene: Lec17-7 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8LK69 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.48 % |
---|---|
Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7.5 Details: 18% 1,4 butanediol, 300 mM Zinc acetate and 0.1 M Imidazole-HCl pH 6-7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2022 |
Radiation | Monochromator: Cu K / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→45.01 Å / Num. obs: 18583 / % possible obs: 98.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 16.8 Å2 / CC1/2: 0.944 / Rmerge(I) obs: 0.21 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.85→1.95 Å / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 2563 / CC1/2: 0.855 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7VUB Resolution: 1.853→44.395 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.841 / WRfactor Rfree: 0.357 / WRfactor Rwork: 0.278 / Average fsc free: 0.9133 / Average fsc work: 0.9423 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.162 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: 18.531 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.853→44.395 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
|