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Yorodumi- PDB-6ifg: Crystal structure of M1 zinc metallopeptidase E323A mutant bound ... -
+Open data
-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 | ||||||
Components |
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Keywords | HYDROLASE / Metalloprotease / peptidase | ||||||
Function / homology | Function and homology information membrane alanyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) Deinococcus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Agrawal, R. / Kumar, A. / Kumar, A. / Makde, R.D. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ifg.cif.gz | 344.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ifg.ent.gz | 279 KB | Display | PDB format |
PDBx/mmJSON format | 6ifg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/6ifg ftp://data.pdbj.org/pub/pdb/validation_reports/if/6ifg | HTTPS FTP |
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-Related structure data
Related structure data | 6a8zSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant) 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: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q9RVZ5 #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.) Deinococcus (bacteria) #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-FMT / #5: 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: 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: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |