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- PDB-1dcn: INACTIVE MUTANT H162N OF DELTA 2 CRYSTALLIN WITH BOUND ARGININOSU... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dcn | ||||||
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Title | INACTIVE MUTANT H162N OF DELTA 2 CRYSTALLIN WITH BOUND ARGININOSUCCINATE | ||||||
![]() | DELTA 2 CRYSTALLIN | ||||||
![]() | EYE LENS PROTEIN / DELTA 2 CRYSTALLIN / ARGININOSUCCINATE LYASE | ||||||
Function / homology | ![]() argininosuccinate lyase / argininosuccinate lyase activity / arginine biosynthetic process via ornithine / structural constituent of eye lens / arginine biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vallee, F. / Turner, M.A. / Lindley, P. / Howell, P.L. | ||||||
![]() | ![]() Title: Crystal structure of an inactive duck delta II crystallin mutant with bound argininosuccinate. Authors: Vallee, F. / Turner, M.A. / Lindley, P.L. / Howell, P.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 338.7 KB | Display | ![]() |
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PDB format | ![]() | 278.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 619 KB | Display | ![]() |
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Full document | ![]() | 676.2 KB | Display | |
Data in XML | ![]() | 40.9 KB | Display | |
Data in CIF | ![]() | 63.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1auwS 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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 49500.797 Da / Num. of mol.: 4 / Mutation: H162N Source method: isolated from a genetically manipulated source Details: ARGININOSUCCINATE BOUND TO ONE ACTIVE SITE / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.7 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 77291 / % possible obs: 90.3 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 27.5 Å2 / Rsym value: 0.079 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.233 |
Reflection | *PLUS Num. measured all: 194258 / Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / % possible obs: 96.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1AUW Resolution: 2.3→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 9791538.7 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.84 Å2 / ksol: 0.346 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3C / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 17 Å / Rfactor Rfree: 0.29 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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