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- PDB-1ifv: CRYSTAL STRUCTURE OF PATHOGENESIS-RELATED PROTEIN LLPR10.1B FROM ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ifv | ||||||
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Title | CRYSTAL STRUCTURE OF PATHOGENESIS-RELATED PROTEIN LLPR10.1B FROM YELLOW LUPINE | ||||||
![]() | PROTEIN LLR18B | ||||||
![]() | ALLERGEN / 7-STRANDED BETA SHEET / C-TERMINAL HELIX | ||||||
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 | ![]() ![]() | ||||||
![]() | Biesiadka, J. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M. | ||||||
![]() | ![]() Title: Crystal structures of two homologous pathogenesis-related proteins from yellow lupine. Authors: Biesiadka, J. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M. #1: ![]() Title: Crystallization and Preliminary X-Ray Structure Determination of Lupinus Luteus Pr10 Protein Authors: Biesiadka, J. / Sikorski, M.M. / Bujacz, G. / Jaskolski, M. #2: ![]() Title: Expression of Genes Encoding Pr10 Class Pathogenesis-Related Proteins is Inhibited in Yellow Lupine Root Nodules Authors: Sikorski, M.M. / Biesiadka, J. / Kasperska, A.E. / Kopcinska, J. / Lotocka, B. / Golinowski, W. / Legocki, A.B. #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. / Joost Van Neerven, R.J. / Schou, C. / Lowenstein, H. / Spangfort, M.D. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE PROTEIN IS MONOMERIC AND THE TWO CHAINS, A AND B, ARE NOT INVOLVED IN QUATERNARY STRUCTURE FORMATION. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 69.5 KB | Display | ![]() |
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PDB format | ![]() | 53.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 16545.537 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||
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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 | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 9, 1999 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. all: 15752 / Num. obs: 15752 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.64 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 13.26 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 3.13 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.78 / Num. unique all: 1498 / % possible all: 94.7 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 15594 / Redundancy: 5.6 % / Num. measured all: 88882 / Rmerge(I) obs: 0.102 |
Reflection shell | *PLUS Lowest resolution: 2.39 Å / % possible obs: 94.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: LlPR10.1A Resolution: 2.25→12 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1857189.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: THE ASYMMETRIC UNIT CONTAINS TWO INDEPENDENT CHAINS, NOT INVOLVED IN QUATERNARY STRUCTURE
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.41 Å2 / ksol: 0.363 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 12 Å / Rfactor all: 0.188 / Rfactor obs: 0.186 / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.186 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.29 / Rfactor Rwork: 0.252 |