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- PDB-1xdf: Crystal structure of pathogenesis-related protein LlPR-10.2A from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xdf | ||||||
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Title | Crystal structure of pathogenesis-related protein LlPR-10.2A from yellow lupine | ||||||
![]() | PR10.2A | ||||||
![]() | PLANT PROTEIN / 7-stranded antiparallel beta-sheet / kinked C-terminal alpha-helix / glycine-rich loop | ||||||
Function / homology | ![]() : / cytokinin binding / response to biotic stimulus / melatonin binding / abscisic acid binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / RNA nuclease activity / defense response ...: / cytokinin binding / response to biotic stimulus / melatonin binding / abscisic acid binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / RNA nuclease activity / defense response / signaling receptor activity / calcium ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pasternak, O. / Biesiadka, J. / Dolot, R. / Handschuh, L. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M. | ||||||
![]() | ![]() Title: Structure of a yellow lupin pathogenesis-related PR-10 protein belonging to a novel subclass. Authors: Pasternak, O. / Biesiadka, J. / Dolot, R. / Handschuh, L. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M. #1: ![]() Title: Crystal structures of two homologous pathogenesis-related proteins from yellow lupine Authors: Biesiadka, J. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M. #2: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1999 Title: Crystallization and preliminary x-ray structure determination of Lupinus luteus PR10 protein Authors: Biesiadka, J. / Sikorski, M.M. / Bujacz, G. / Jaskolski, M. #3: ![]() Title: X-ray and NMR structure of Bet v 1, the origin of birch pollen allergy Authors: Gajhede, M. / Osmark, P. / Poulsen, F.M. / Ipsen, H. / Larsen, J.N. / van Neerven, R.J.J. / Schou, C. / Lowenstein, H. / Spangfort, M.D. #4: ![]() Title: Crystal structure of a hypoallergenic isoform of the major birch pollen allergen Bet v 1 and its likely biological function as a plant steroid carrier Authors: Markovic-Housley, Z. / Degano, M. / Lamba, D. / von Roepenack-Lahaye, E. / Clemens, S. / Susani, M. / Ferreira, F. / Scheiner, O. / Breiteneder, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.9 KB | Display | ![]() |
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PDB format | ![]() | 59.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.6 KB | Display | ![]() |
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Full document | ![]() | 456.6 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ifvS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. THE PROTEIN IS MONOMERIC AND THE TWO CHAINS, A AND B, ARE NOT INVOLVED IN QUATERNARY STRUCTURE FORMATION. |
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Components
#1: Protein | Mass: 16792.824 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NA / | #3: Chemical | ChemComp-EPE / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.2 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: sodium citrate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 10, 2000 / Details: mirrors |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 30830 / Num. obs: 30830 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3000 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1IFV Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.413 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: H ATOMS AT RIDING POSITIONS WERE INCLUDED IN FC CALCULATIONS; ONE OF THE TWO PROTEIN MOLECULES COORDINATES A SODIUM CATION; THE REFINEMENT INCLUDED TLS PARAMETERS; THE TIPS OF 6 SURFACE ...Details: H ATOMS AT RIDING POSITIONS WERE INCLUDED IN FC CALCULATIONS; ONE OF THE TWO PROTEIN MOLECULES COORDINATES A SODIUM CATION; THE REFINEMENT INCLUDED TLS PARAMETERS; THE TIPS OF 6 SURFACE RESIDUES (1 IN MOL. A, 5 IN MOL. B) HAVE NOT BEEN MEDELED BECAUSE OF MISSING ELECTRON DENSITY, AND THE CORRESPONDING ATOMS ARE NOT INCLUDED IN THE MODEL (SEE REMARK 470);
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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: 24.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / 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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