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- PDB-1icx: CRYSTAL STRUCTURE OF PATHOGENESIS-RELATED PROTEIN LLPR10.1A FROM ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1icx | ||||||
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Title | CRYSTAL STRUCTURE OF PATHOGENESIS-RELATED PROTEIN LLPR10.1A FROM YELLOW LUPINE | ||||||
![]() | PROTEIN LLR18A | ||||||
![]() | 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 / signaling receptor activity ...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 / nucleus / 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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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43.9 KB | Display | ![]() |
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PDB format | ![]() | 30.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.4 KB | Display | ![]() |
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Full document | ![]() | 429.3 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ifvC ![]() 1btvS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
#1: Protein | Mass: 16748.924 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.8 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonium sulfate, TRIS, sucrose laureate, pH 8.0, 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 17, 1999 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.375 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→19.35 Å / Num. obs: 9446 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 9.46 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.73 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 8.46 / % possible all: 96.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Redundancy: 9.5 % / Num. measured all: 89375 / Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS Lowest resolution: 2.07 Å / % possible obs: 96.8 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 8.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BTV Resolution: 1.95→12 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: RESIDUES ASP 60, GLN 133, LYS 135, PHE 136 REFINED AS ALANINES BECAUSE OF POOR SIDE-CHAIN ELECTRON DENSITY
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.41 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 12 Å / % reflection Rfree: 10 % / Rfactor obs: 0.196 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.196 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.285 / Rfactor Rwork: 0.212 |