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- PDB-4g1p: Structural and Mechanistic Basis of Substrate Recognition by Nove... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4g1p | ||||||
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Title | Structural and Mechanistic Basis of Substrate Recognition by Novel Di-peptidase Dug1p From Saccharomyces cerevisiae | ||||||
![]() | Cys-Gly metallodipeptidase DUG1 | ||||||
![]() | HYDROLASE / Di-nuclear peptidases / M20 family metallo-peptidases / alpha/beta scaffold / N-terminal catalytic domain/C-terminal lid domain | ||||||
Function / homology | ![]() Glutathione synthesis and recycling / Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / glutathione catabolic process / metallodipeptidase activity / peptidase activity / omega peptidase activity / mitochondrion / proteolysis / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Singh, A.K. / Singh, M. / Pandya, V.K. / Singh, V. / Mittal, M. / Kumaran, S. | ||||||
![]() | ![]() Title: Structural and Mechanistic Basis of Substrate Recognition by Novel Di-peptidase Dug1p From Saccromyces cerevesiae Authors: Singh, A.K. / Singh, M. / Pandya, V.K. / Singh, V. / Mittal, M. / Kumaran, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.7 KB | Display | ![]() |
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PDB format | ![]() | 83 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.6 KB | Display | ![]() |
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Full document | ![]() | 462.9 KB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zofS 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 53760.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S288c / Gene: Dug1p / Plasmid: pET23a / Production host: ![]() ![]() References: UniProt: P43616, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-GLY / | #4: Chemical | ChemComp-CYS / | #5: Water | ChemComp-HOH / | Nonpolymer details | DI-PEPTIDE, GLY-CYS IS INTRINSIC DIPEPTIDE. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.95 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.5 M AmSO4, 0.1 M tri-Na citrate pH 5.6, 1.0 M Lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 16, 2010 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.547→50 Å / Num. obs: 24507 / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Biso Wilson estimate: 36.42 Å2 / Rmerge(I) obs: 0.216 |
Reflection shell | Resolution: 2.55→2.7 Å / Redundancy: 11.21 % / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 2.27 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZOF Resolution: 2.547→19.731 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.841 / SU ML: 0.32 / σ(F): 1.99 / Phase error: 22.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.74 Å2 / Biso mean: 36.42 Å2 / Biso min: 10.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.547→19.731 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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