+Open data
-Basic information
Entry | Database: PDB / ID: 7ksb | ||||||
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Title | Crystal structure on Act c 10.0101 | ||||||
Components | Non-specific lipid-transfer protein 1 | ||||||
Keywords | ALLERGEN / nsLTP / food allergen | ||||||
Function / homology | Plant non-specific lipid-transfer protein/Par allergen / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / lipid transport / lipid binding / Non-specific lipid-transfer protein 1 Function and homology information | ||||||
Biological species | Actinidia chinensis var. chinensis (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Pote, S. / O'Malley, A. / Gawlicka-Chruszcz, A. / Giangrieco, I. / Ciardiello, M.A. / Chruszcz, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Molecules / Year: 2021 Title: Structural Characterization of Act c 10.0101 and Pun g 1.0101-Allergens from the Non-Specific Lipid Transfer Protein Family. Authors: O'Malley, A. / Pote, S. / Giangrieco, I. / Tuppo, L. / Gawlicka-Chruszcz, A. / Kowal, K. / Ciardiello, M.A. / Chruszcz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ksb.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ksb.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ksb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/7ksb ftp://data.pdbj.org/pub/pdb/validation_reports/ks/7ksb | HTTPS FTP |
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-Related structure data
Related structure data | 7kscC 1rzlS 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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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 1 - 92 / Label seq-ID: 1 - 92
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-Components
#1: Protein | Mass: 9472.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Actinidia chinensis var. chinensis (plant) References: UniProt: P85204 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 1.87 Å3/Da / Density % sol: 34.16 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 4 Details: 0.1 M citric acid buffer, pH 4.0 with 3.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→40 Å / Num. obs: 10217 / % possible obs: 98.7 % / Redundancy: 4 % / Rpim(I) all: 0.057 / Rrim(I) all: 0.113 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 4.3 / Num. unique obs: 497 / CC1/2: 0.904 / Rpim(I) all: 0.24 / Rrim(I) all: 0.483 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RZL Resolution: 1.95→27.91 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / SU B: 10.241 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.19 Å2 / Biso mean: 26.802 Å2 / Biso min: 15.24 Å2
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Refinement step | Cycle: final / Resolution: 1.95→27.91 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 2528 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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