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- PDB-1q9b: CRYSTAL STRUCTURE ANALYSIS OF Hev b 6.02 (HEVEIN) AT 1.5 ANGSTROM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1q9b | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF Hev b 6.02 (HEVEIN) AT 1.5 ANGSTROMS RESOLUTION | ||||||
![]() | Hevein | ||||||
![]() | ALLERGEN / LECTIN / AGGLUTININ-TOXIN MOTIF | ||||||
Function / homology | ![]() chitin binding / RNA nuclease activity / defense response to fungus / defense response to bacterium Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rodriguez-Romero, A. / Hernandez-Santoyo, A. | ||||||
![]() | ![]() Title: Insights into a conformational epitope of Hev b 6.02 (hevein). Authors: Reyes-Lopez, C.A. / Hernandez-Santoyo, A. / Pedraza-Escalona, M. / Mendoza, G. / Hernandez-Arana, A. / Rodriguez-Romero, A. #1: ![]() Title: Crystal Structure of Hevein at 2.8 A Resolution Authors: Rodriguez-Romero, A. / Ravichandran, K.G. / Soriano-Garcia, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 32.8 KB | Display | ![]() |
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PDB format | ![]() | 21.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.3 KB | Display | ![]() |
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Full document | ![]() | 436.9 KB | Display | |
Data in XML | ![]() | 5 KB | Display | |
Data in CIF | ![]() | 6.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hevS 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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Unit cell |
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Components
#1: Protein/peptide | Mass: 4731.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.5 % | ||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: MPD, Tris-HCl, pH 7.10, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.1 / Method: vapor diffusion, sitting drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1999 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→15 Å / Num. all: 7678 / Num. obs: 7332 / % possible obs: 95.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 13.9 Å2 / Rsym value: 0.05 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 12.3 / Num. unique all: 635 / Rsym value: 0.046 / % possible all: 97.2 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 15 Å / Num. obs: 7113 / Redundancy: 4.7 % / Num. measured all: 57822 / Rmerge(I) obs: 0.05 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HEV Resolution: 1.5→9.5 Å / Num. parameters: 3772 / Num. restraintsaints: 4884 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: THE ALTERNATE CONFORMATIONS EVENTUALLY REDUCED FREE R FROM 21.19-19.20%. INTRODUCTION OF ANISOTROPIC REFINEMENT REDUCED FREE R FROM 19.20- 16.01%. DISCRETELY DISORDERED HETEROGENS: 2, MPD ...Details: THE ALTERNATE CONFORMATIONS EVENTUALLY REDUCED FREE R FROM 21.19-19.20%. INTRODUCTION OF ANISOTROPIC REFINEMENT REDUCED FREE R FROM 19.20- 16.01%. DISCRETELY DISORDERED HETEROGENS: 2, MPD 101 AND MPD 102; DISCRETELY DISORDERED RESIDUES: 6, GLU 1, LEU 11, PRO 13, SER 26, GLU 29, PRO 33. ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 8 / Occupancy sum hydrogen: 268 / Occupancy sum non hydrogen: 379 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→9.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.53 Å / Num. reflection Rfree: 63 / Num. reflection obs: 635 | |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rwork: 0.128 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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