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- PDB-3iir: Crystal Structure of Miraculin like protein from seeds of Murraya... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3iir | ||||||
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Title | Crystal Structure of Miraculin like protein from seeds of Murraya koenigii | ||||||
![]() | Trypsin inhibitor | ||||||
![]() | HYDROLASE INHIBITOR / beta-trefoil fold / Kunitz trypsin inhibitor | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gahloth, D. / Selvakumar, P. / Shee, C. / Kumar, P. / Sharma, A.K. | ||||||
![]() | ![]() Title: Cloning, sequence analysis and crystal structure determination of a miraculin-like protein from Murraya koenigii Authors: Gahloth, D. / Selvakumar, P. / Shee, C. / Kumar, P. / Sharma, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.8 KB | Display | ![]() |
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PDB format | ![]() | 64.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432 KB | Display | ![]() |
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Full document | ![]() | 446.2 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1avaS 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 | Mass: 20759.291 Da / Num. of mol.: 2 / Fragment: UNP residues 26-215 / Source method: isolated from a natural source / Details: Seeds / Source: (natural) ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 6% PEG 8000, 0.1mM Tris-Cl pH 8.0, 0.08M Sodium Chloride, 0.08M Calcium Chloride, 8% Glycerol , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 26, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→25 Å / Num. obs: 10300 / % possible obs: 96.1 % / Observed criterion σ(I): 58581 / Redundancy: 5.6 % / Biso Wilson estimate: 51.9 Å2 / Rmerge(I) obs: 0.146 / Rsym value: 0.146 / Net I/σ(I): 4.7 / Num. measured all: 58581 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 4.7 / Num. unique all: 540 / Rsym value: 0.422 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1AVA Resolution: 2.9→10 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.835 / SU B: 17.851 / SU ML: 0.347 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.497 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: weighted full matrix least squares procedure
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.074 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.969 Å / Total num. of bins used: 20
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