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- PDB-6ifg: Crystal structure of M1 zinc metallopeptidase E323A mutant bound ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ifg | ||||||
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Title | Crystal structure of M1 zinc metallopeptidase E323A mutant bound to Tyr-ser-ala substrate from Deinococcus radiodurans | ||||||
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![]() | HYDROLASE / Metalloprotease / peptidase | ||||||
Function / homology | ![]() membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / peptide binding / proteolysis / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Agrawal, R. / Kumar, A. / Kumar, A. / Makde, R.D. | ||||||
![]() | ![]() Title: Two-domain aminopeptidase of M1 family: Structural features for substrate binding and gating in absence of C-terminal domain. Authors: Agrawal, R. / Goyal, V.D. / Kumar, A. / Gaur, N.K. / Jamdar, S.N. / Kumar, A. / 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 | ![]() | 344.2 KB | Display | ![]() |
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PDB format | ![]() | 279 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 33.1 KB | Display | |
Data in CIF | ![]() | 47.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6a8zSC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51547.793 Da / Num. of mol.: 2 / Mutation: E323A 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_0875 / Plasmid: pST50TR / Details (production host): pET3a based / Production host: ![]() ![]() #2: Protein/peptide | Mass: 339.345 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The peptide substrate sequence is designed and synthesized based on the enzymatic assay of the M1 metallopeptidase from Deinococcus radiodurans Source: (synth.) ![]() #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.03 % / Description: Plate like crystals |
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Crystal grow | Temperature: 294 K / Method: microbatch / pH: 5.5 Details: 0.2M Ammonium formate, 0.1M Bis-tris pH 5.5, 25% PEG 3350 PH range: 5.5-7.0 |
-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: Jul 28, 2018 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.83 Å / Num. obs: 56301 / % possible obs: 97.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 13.046 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.039 / Rrim(I) all: 0.065 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3603 / CC1/2: 0.865 / Rpim(I) all: 0.269 / Rrim(I) all: 0.446 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6A8Z Resolution: 1.9→24.137 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→24.137 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: -41.9149 Å / Origin y: -40.7837 Å / Origin z: 5.5599 Å
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Refinement TLS group | Selection details: all |