+Open data
-Basic information
Entry | Database: PDB / ID: 1x1v | ||||||
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Title | Structure Of Banana Lectin- Methyl-Alpha-Mannose Complex | ||||||
Components | lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / all beta sheet protein / beta prism-I fold / mannose specific | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Musa acuminata (dwarf banana) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Singh, D.D. / Saikrishnan, K. / Kumar, P. / Surolia, A. / Sekar, K. / Vijayan, M. | ||||||
Citation | Journal: Glycobiology / Year: 2005 Title: Unusual sugar specificity of banana lectin from Musa paradisiaca and its probable evolutionary origin. Crystallographic and modelling studies Authors: Singh, D.D. / Saikrishnan, K. / Kumar, P. / Surolia, A. / Sekar, K. / Vijayan, M. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004 Title: Purification, crystallization and preliminary X-ray structure analysis of the banana lectin from Musa paradisiaca Authors: Singh, D.D. / Saikrishnan, K. / Kumar, P. / Dauter, Z. / Sekar, K. / Surolia, A. / Vijayan, M. #2: Journal: J.Mol.Biol. / Year: 2004 Title: Structural basis for the carbohydrate specificities of artocarpin: variation in the length of a loop as a strategy for generating ligand specificity Authors: Jeyaprakash, A.A. / Srivastav, A. / Surolia, A. / Vijayan, M. #3: Journal: J.Mol.Biol. / Year: 2002 Title: Crystal structures of artocarpin, a Moraceae lectin with mannose specificity, and its complex with methyl-alpha-D-mannose: implications to the generation of carbohydrate specificity Authors: Pratap, J.V. / Jeyaprakash, A.A. / Rani, P.G. / Sekar, K. / Surolia, A. / Vijayan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x1v.cif.gz | 82.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x1v.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 1x1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/1x1v ftp://data.pdbj.org/pub/pdb/validation_reports/x1/1x1v | HTTPS FTP |
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-Related structure data
Related structure data | 1c3nS 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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Details | The biological assembly is a dimer as contained in the asymmetric unit |
-Components
#1: Protein | Mass: 14683.493 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: synonym: musa paradisiaca / Source: (natural) Musa acuminata (dwarf banana) / References: UniProt: Q8L5H4 #2: Sugar | ChemComp-MMA / #3: Chemical | #4: Chemical | ChemComp-HEZ / #5: Water | ChemComp-HOH / | |
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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: 4.7 Å3/Da / Density % sol: 73.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: zinc acetate dihydrate, sodium cacodylate, 1,6-hexanediol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 4, 2004 / Details: mirrors |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→30 Å / Num. all: 21859 / Num. obs: 21617 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.07 |
Reflection shell | Resolution: 2.45→2.54 Å / Rmerge(I) obs: 0.533 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C3N Resolution: 2.45→24.92 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.912 / SU B: 17.375 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.216 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→24.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.513 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 26.0618 Å / Origin y: 23.1978 Å / Origin z: 58.4053 Å
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Refinement TLS group |
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