+Open data
-Basic information
Entry | Database: PDB / ID: 4piu | ||||||
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Title | CRYSTAL STRUCTURE OF BANANA LECTIN H84T MUTANT | ||||||
Components | Ripening-associated protein | ||||||
Keywords | SUGAR BINDING PROTEIN / JACALIN-LIKE LECTIN DOMAIN / LECTIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Musa acuminata (dwarf banana) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Meagher, J.L. / Stuckey, J.A. | ||||||
Citation | Journal: Cell / Year: 2015 Title: Engineering a Therapeutic Lectin by Uncoupling Mitogenicity from Antiviral Activity. Authors: Swanson, M.D. / Boudreaux, D.M. / Salmon, L. / Chugh, J. / Winter, H.C. / Meagher, J.L. / Andre, S. / Murphy, P.V. / Oscarson, S. / Roy, R. / King, S. / Kaplan, M.H. / Goldstein, I.J. / ...Authors: Swanson, M.D. / Boudreaux, D.M. / Salmon, L. / Chugh, J. / Winter, H.C. / Meagher, J.L. / Andre, S. / Murphy, P.V. / Oscarson, S. / Roy, R. / King, S. / Kaplan, M.H. / Goldstein, I.J. / Tarbet, E.B. / Hurst, B.L. / Smee, D.F. / de la Fuente, C. / Hoffmann, H.H. / Xue, Y. / Rice, C.M. / Schols, D. / Garcia, J.V. / Stuckey, J.A. / Gabius, H.J. / Al-Hashimi, H.M. / Markovitz, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4piu.cif.gz | 126.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4piu.ent.gz | 98.9 KB | Display | PDB format |
PDBx/mmJSON format | 4piu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/4piu ftp://data.pdbj.org/pub/pdb/validation_reports/pi/4piu | HTTPS FTP |
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-Related structure data
Related structure data | 4pifC 4pikC 4pitC 2bmyS S: Starting model for refinement C: citing same article (ref.) |
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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: 14724.607 Da / Num. of mol.: 2 / Mutation: H84T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Musa acuminata (dwarf banana) / Production host: Escherichia coli (E. coli) / References: UniProt: O22321 #2: Chemical | ChemComp-NA / | #3: Chemical | ChemComp-GOL / #4: 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: 2.42 Å3/Da / Density % sol: 49.17 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / Details: 20% PEG8000, 0.05 M POTASSIUM PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97853 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 21, 2010 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 38133 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.472 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BMY Resolution: 1.6→25.31 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.568 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.076 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→25.31 Å
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Refine LS restraints |
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