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- PDB-6iru: Crystal structure of Peptidase E from Deinococcus radiodurans in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6iru | ||||||
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Title | Crystal structure of Peptidase E from Deinococcus radiodurans in P6422 space group | ||||||
![]() | peptidase DR_1070 | ||||||
![]() | HYDROLASE / S51 peptidase / peptidase E / dimer / active site / esterase | ||||||
Function / homology | Peptidase S51 / Peptidase family S51 / Class I glutamine amidotransferase-like / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / proteolysis / Uncharacterized peptidase DR_1070![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yadav, P. / Chandravanshi, K. / Kumar, A. / Makde, R.D. | ||||||
![]() | ![]() Title: Catalytic triad heterogeneity in S51 peptidase family: Structural basis for functional variability. Authors: Yadav, P. / Goyal, V.D. / Chandravanshi, K. / Kumar, A. / Gokhale, S.M. / Jamdar, S.N. / Makde, R.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 229.7 KB | Display | ![]() |
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PDB format | ![]() | 186 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.3 KB | Display | ![]() |
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Full document | ![]() | 447.6 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6a4tSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22729.799 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 Gene: DR_1070 / Plasmid: pet28a / Production host: ![]() ![]() References: UniProt: Q9RVF9, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density meas: 54.32 Mg/m3 / Density % sol: 58.57 % / Description: hexagonal shape (200-250 micron) |
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Crystal grow | Temperature: 294 K / Method: microbatch / pH: 6.5 / Details: 0.1 M Bis-tris pH 6.5, 25 % PEG3350 / PH range: 5.5-7.5 |
-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: Sep 15, 2018 / Details: mirrors |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→48.14 Å / Num. obs: 23227 / % possible obs: 100 % / Redundancy: 14.5 % / Biso Wilson estimate: 58.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.028 / Rrim(I) all: 0.11 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 2.7→2.83 Å / Redundancy: 14.9 % / Rmerge(I) obs: 1.147 / Num. unique obs: 3029 / CC1/2: 0.909 / Rpim(I) all: 0.297 / Rrim(I) all: 1.186 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6A4T Resolution: 2.7→16.026 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→16.026 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 17.4828 Å / Origin y: -67.2766 Å / Origin z: 11.1551 Å
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Refinement TLS group | Selection details: all |