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Yorodumi- PDB-1i0a: CRYSTAL STRUCTURE OF WILD TYPE TURKEY DELTA 1 CRYSTALLIN (EYE LEN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i0a | ||||||
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Title | CRYSTAL STRUCTURE OF WILD TYPE TURKEY DELTA 1 CRYSTALLIN (EYE LENS PROTEIN) | ||||||
Components | DELTA CRYSTALLIN I | ||||||
Keywords | LYASE / EYE LENS PROTEIN / DELTA 1 CRYSTALLIN / ARGININOSUCCINATE LYASE | ||||||
Function / homology | Function and homology information arginine biosynthetic process via ornithine / structural constituent of eye lens Similarity search - Function | ||||||
Biological species | Meleagris gallopavo (turkey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å | ||||||
Authors | Sampaleanu, L.M. / Vallee, F. / Slingsby, C. / Howell, P.L. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Structural studies of duck delta 1 and delta 2 crystallin suggest conformational changes occur during catalysis. Authors: Sampaleanu, L.M. / Vallee, F. / Slingsby, C. / Howell, P.L. #1: Journal: Nat.Struct.Biol. / Year: 1994 Title: The structure of avian eye lens delta-crystallin reveals a new fold for a superfamily of oligomeric enzymes Authors: Simpson, A. / Bateman, O. / Driessen, H. / Lindley, P. / Moss, D. / Mylvaganam, S. / Narebor, E. / Slingsby, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i0a.cif.gz | 347.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i0a.ent.gz | 286.9 KB | Display | PDB format |
PDBx/mmJSON format | 1i0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i0a_validation.pdf.gz | 460.5 KB | Display | wwPDB validaton report |
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Full document | 1i0a_full_validation.pdf.gz | 500.5 KB | Display | |
Data in XML | 1i0a_validation.xml.gz | 69.6 KB | Display | |
Data in CIF | 1i0a_validation.cif.gz | 96.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/1i0a ftp://data.pdbj.org/pub/pdb/validation_reports/i0/1i0a | HTTPS FTP |
-Related 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 tetramer present in the asymmetric unit |
-Components
#1: Protein | Mass: 50892.707 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: ISOLATED FROM 1 DAY OLD TURKEY EYE LENSES / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: Q7SIE0, argininosuccinate lyase #2: 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: 2.46 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 0.1M calcium acetate, 7-15% PEG 6000, argininosuccinate, pH 4.7, VAPOR DIFFUSION, HANGING DROP at 293 K |
Crystal grow | *PLUS |
-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 30, 1993 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 68630 / Num. obs: 68630 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.052 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.5→19.78 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3157643.59 / 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: 65.57 Å2 / ksol: 0.314 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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