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Yorodumi- PDB-1tjw: Crystal Structure of T161D Duck Delta 2 Crystallin Mutant with bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tjw | ||||||
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Title | Crystal Structure of T161D Duck Delta 2 Crystallin Mutant with bound argininosuccinate | ||||||
Components | Delta crystallin II | ||||||
Keywords | LYASE / eye lens protein / delta 2 crystallin / argininosuccinate lyase / enzyme mechanism | ||||||
Function / homology | Function and homology information argininosuccinate lyase / argininosuccinate lyase activity / arginine biosynthetic process via ornithine / structural constituent of eye lens / arginine biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Anas platyrhynchos (mallard) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Sampaleanu, L.M. / Codding, P.W. / Lobsanov, Y.D. / Tsai, M. / Smith, G.D. / Horvatin, C. / Howell, P.L. | ||||||
Citation | Journal: Biochem.J. / Year: 2004 Title: Structural studies of duck delta2 crystallin mutants provide insight into the role of Thr161 and the 280s loop in catalysis Authors: Sampaleanu, L.M. / Codding, P.W. / Lobsanov, Y.D. / Tsai, M. / Smith, G.D. / Horvatin, C. / 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 | 1tjw.cif.gz | 362.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tjw.ent.gz | 294.8 KB | Display | PDB format |
PDBx/mmJSON format | 1tjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/1tjw ftp://data.pdbj.org/pub/pdb/validation_reports/tj/1tjw | HTTPS FTP |
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-Related structure data
Related structure data | 1tjuC 1tjvC 1hy1S 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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Details | The biological assembly is the homotetramer with four bound argininosuccinate molecules, as present in the assymetric unit |
-Components
#1: Protein | Mass: 52616.234 Da / Num. of mol.: 4 / Fragment: Duck delta 2 crystallin / Mutation: T161D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anas platyrhynchos (mallard) / Production host: Escherichia coli (E. coli) / Strain (production host): plasmid / References: UniProt: P24058, argininosuccinate lyase #2: Chemical | ChemComp-AS1 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 14% PEG2000 MME, 350 mM magnesium chloride, 100 mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2001 |
Radiation | Monochromator: parabolic collimating mirror placed upstream of the monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2→41.8 Å / Num. all: 141060 / Num. obs: 128293 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 12 Å2 / Rsym value: 0.063 |
Reflection shell | Resolution: 2→2.07 Å / Rsym value: 0.2 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1HY1 Resolution: 2→41.76 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 256303.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.7916 Å2 / ksol: 0.356132 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→41.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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