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Yorodumi- PDB-1z3q: Resolution of the structure of the allergenic and antifungal bana... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z3q | ||||||
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Title | Resolution of the structure of the allergenic and antifungal banana fruit thaumatin-like protein at 1.7A | ||||||
Components | Thaumatin-like Protein | ||||||
Keywords | ANTIFUNGAL PROTEIN / beta sandwich | ||||||
Function / homology | Function and homology information Thaumatin / Thaumatin / Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Musa acuminata (dwarf banana) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Leone, P. / Menu-Bouaouiche, L. / Peumans, W.J. / Barre, A. / Payan, F. / Roussel, A. / Van Damme, E.J.M. / Rouge, P. | ||||||
Citation | Journal: Biochimie / Year: 2006 Title: Resolution of the structure of the allergenic and antifungal banana fruit thaumatin-like protein at 1.7-A Authors: Leone, P. / Menu-Bouaouiche, L. / Peumans, W.J. / Payan, F. / Barre, A. / Roussel, A. / Van Damme, E.J.M. / Rouge, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z3q.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z3q.ent.gz | 39.6 KB | Display | PDB format |
PDBx/mmJSON format | 1z3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z3q_validation.pdf.gz | 415.1 KB | Display | wwPDB validaton report |
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Full document | 1z3q_full_validation.pdf.gz | 415.6 KB | Display | |
Data in XML | 1z3q_validation.xml.gz | 12 KB | Display | |
Data in CIF | 1z3q_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/1z3q ftp://data.pdbj.org/pub/pdb/validation_reports/z3/1z3q | HTTPS FTP |
-Related structure data
Related structure data | 1thvS 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: 21245.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Musa acuminata (dwarf banana) / Tissue: pulp / References: UniProt: O22322 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, Ammonium Sulfate, Sodium Acatate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-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: Feb 2, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→42.2 Å / Num. all: 20728 / Num. obs: 20095 / % possible obs: 96.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 15.31 Å2 / Rsym value: 0.042 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 9.4 / Num. unique all: 1920 / Rsym value: 0.131 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1THV Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.547 / SU ML: 0.053 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.094 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.877 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / Total num. of bins used: 20
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