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Yorodumi- PDB-1dcn: INACTIVE MUTANT H162N OF DELTA 2 CRYSTALLIN WITH BOUND ARGININOSU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dcn | ||||||
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Title | INACTIVE MUTANT H162N OF DELTA 2 CRYSTALLIN WITH BOUND ARGININOSUCCINATE | ||||||
Components | DELTA 2 CRYSTALLIN | ||||||
Keywords | EYE LENS PROTEIN / DELTA 2 CRYSTALLIN / ARGININOSUCCINATE LYASE | ||||||
Function / homology | Function and homology information argininosuccinate lyase / argininosuccinate lyase activity / arginine biosynthetic process via ornithine / structural constituent of eye lens / arginine biosynthetic process Similarity search - Function | ||||||
Biological species | Anas platyrhynchos (mallard) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Vallee, F. / Turner, M.A. / Lindley, P. / Howell, P.L. | ||||||
Citation | Journal: Biochemistry / Year: 1999 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dcn.cif.gz | 334.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dcn.ent.gz | 278.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/1dcn ftp://data.pdbj.org/pub/pdb/validation_reports/dc/1dcn | HTTPS FTP |
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-Related structure data
Related structure data | 1auwS S: Starting model for refinement |
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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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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.) Anas platyrhynchos (mallard) / Cell line: 293 / Organ: EYE / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P24058, argininosuccinate lyase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91 |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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