+Open data
-Basic information
Entry | Database: PDB / ID: 1k7w | ||||||
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Title | Crystal Structure of S283A Duck Delta 2 Crystallin Mutant | ||||||
Components | delta 2 crystallin | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Sampaleanu, L.M. / Yu, B. / Howell, P.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Mutational analysis of duck delta 2 crystallin and the structure of an inactive mutant with bound substrate provide insight into the enzymatic mechanism of argininosuccinate lyase. Authors: Sampaleanu, L.M. / Yu, B. / 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 | 1k7w.cif.gz | 359.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k7w.ent.gz | 293.8 KB | Display | PDB format |
PDBx/mmJSON format | 1k7w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k7w_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1k7w_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1k7w_validation.xml.gz | 74.1 KB | Display | |
Data in CIF | 1k7w_validation.cif.gz | 102.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/1k7w ftp://data.pdbj.org/pub/pdb/validation_reports/k7/1k7w | HTTPS FTP |
-Related structure data
Related structure data | 1hy1S 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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Details | The biological assembly is the homotetramer with four bound argininosuccinate molecules, as present in the asymmetric unit |
-Components
#1: Protein | Mass: 51743.355 Da / Num. of mol.: 4 / Mutation: S283A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anas platyrhynchos (mallard) / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BB101 / 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: 2.32 Å3/Da / Density % sol: 47.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% PEG 2000 MME, 300 mM magnesium chloride, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.96 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 18, 2000 |
Radiation | Monochromator: parabolic collimating mirror placed upstream of crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→20 Å / Num. all: 125073 / Num. obs: 125073 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 16.8 Å2 / Rsym value: 0.08 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.96→2.03 Å / Rsym value: 0.34 / % possible all: 91.8 |
Reflection | *PLUS Highest resolution: 1.94 Å / Lowest resolution: 20 Å / Num. obs: 127416 / % possible obs: 94 % / Num. measured all: 692205 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 91.8 % / Rmerge(I) obs: 0.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HY1 Resolution: 1.96→19.81 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 299780.83 / 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: 57.7155 Å2 / ksol: 0.393911 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 30 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.96→19.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.08 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.207 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.03 Å / Rfactor Rfree: 0.301 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.257 |