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Yorodumi- PDB-4z2f: Sclerotium Rolfsii lectin variant (SSR2) with fine carbohydrate s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z2f | ||||||
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Title | Sclerotium Rolfsii lectin variant (SSR2) with fine carbohydrate specificity | ||||||
Components | lectin variant 2 | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin / carbohydrate-binding specificity | ||||||
Function / homology | Fungal fruit body lectin / Fungal fruit body lectin / Cytolysin/lectin / Cytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / Sandwich / Mainly Beta / Lectin variant 2 Function and homology information | ||||||
Biological species | Athelia rolfsii (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kantsadi, A.L. / Peppa, V.I. / Leonidas, D.D. | ||||||
Citation | Journal: Molecules / Year: 2015 Title: Molecular Cloning, Carbohydrate Specificity and the Crystal Structure of Two Sclerotium rolfsii Lectin Variants. Authors: Peppa, V.I. / Venkat, H. / Kantsadi, A.L. / Inamdar, S.R. / Bhat, G.G. / Eligar, S. / Shivanand, A. / Chachadi, V.B. / Satisha, G.J. / Swamy, B.M. / Skamnaki, V.T. / Zographos, S.E. / Leonidas, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z2f.cif.gz | 74.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z2f.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 4z2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/4z2f ftp://data.pdbj.org/pub/pdb/validation_reports/z2/4z2f | HTTPS FTP |
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-Related structure data
Related structure data | 4yldC 4z2qC 4z2sC 2ofdS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16177.888 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Athelia rolfsii (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M3KL31*PLUS #2: Chemical | ChemComp-MPD / ( | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.23 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 8.5 / Details: 20% v/v MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54178 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Feb 25, 2013 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→13.56 Å / Num. obs: 43553 / % possible obs: 100 % / Redundancy: 5.6 % / Rsym value: 0.08 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OFD Resolution: 2.5→13.56 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→13.56 Å
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Refine LS restraints |
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LS refinement shell |
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