+Open data
-Basic information
Entry | Database: PDB / ID: 2i0w | ||||||
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Title | Crystal structure analysis of NP24-I, a thaumatin-like protein | ||||||
Components | Protein NP24 | ||||||
Keywords | ANTIFUNGAL PROTEIN / alpha-beta protein | ||||||
Function / homology | Function and homology information defense response to fungus / defense response / killing of cells of another organism / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Solanum lycopersicum (tomato) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Chakrabarti, C. / Ghosh, R. | ||||||
Citation | Journal: Planta / Year: 2008 Title: Crystal structure analysis of NP24-I: a thaumatin-like protein Authors: Ghosh, R. / Chakrabarti, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i0w.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i0w.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 2i0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i0w_validation.pdf.gz | 425.4 KB | Display | wwPDB validaton report |
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Full document | 2i0w_full_validation.pdf.gz | 427.9 KB | Display | |
Data in XML | 2i0w_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 2i0w_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/2i0w ftp://data.pdbj.org/pub/pdb/validation_reports/i0/2i0w | HTTPS FTP |
-Related structure data
Related structure data | 1pcvS 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: 22232.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ripe tomato / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: P12670 |
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#2: Chemical | ChemComp-CL / |
#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: 2.63 Å3/Da / Density % sol: 53.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 0.1M lithium chloride, 20% PEG 3350, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 7, 2005 / Details: Osmic multilayers |
Radiation | Monochromator: osmic multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→20 Å / Num. obs: 8574 / % possible obs: 99.9 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 4.06 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 2.45→2.51 Å / Redundancy: 4.04 % / Rmerge(I) obs: 0.3369 / Mean I/σ(I) obs: 1.5 / Num. unique all: 567 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PCV Resolution: 2.5→19.83 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 988975.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.1517 Å2 / ksol: 0.305957 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.6 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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