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Yorodumi- PDB-1icx: CRYSTAL STRUCTURE OF PATHOGENESIS-RELATED PROTEIN LLPR10.1A FROM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1icx | ||||||
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Title | CRYSTAL STRUCTURE OF PATHOGENESIS-RELATED PROTEIN LLPR10.1A FROM YELLOW LUPINE | ||||||
Components | PROTEIN LLR18A | ||||||
Keywords | ALLERGEN / 7-stranded beta sheet / C-terminal helix | ||||||
Function / homology | Function and homology information 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 / cytosol Similarity search - Function | ||||||
Biological species | Lupinus luteus (yellow lupine) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Biesiadka, J. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystal structures of two homologous pathogenesis-related proteins from yellow lupine. Authors: Biesiadka, J. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M. #1: 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. #2: Journal: Plant Sci. / Year: 1999 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: Journal: Nat.Struct.Biol. / Year: 1996 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1icx.cif.gz | 43.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1icx.ent.gz | 30.3 KB | Display | PDB format |
PDBx/mmJSON format | 1icx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/1icx ftp://data.pdbj.org/pub/pdb/validation_reports/ic/1icx | HTTPS FTP |
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-Related structure data
Related structure data | 1ifvC 1btvS 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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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.) Lupinus luteus (yellow lupine) / Plasmid: PET3A-LLPR10.1A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P52778 |
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#2: 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: 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: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |