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Yorodumi- PDB-6kp1: Crystal structure of two domain M1 zinc metallopeptidase E323A mu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kp1 | ||||||
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Title | Crystal structure of two domain M1 zinc metallopeptidase E323A mutant bound to L-methionine amino acid | ||||||
Components | Zinc metalloprotease, putativeMetalloproteinase | ||||||
Keywords | HYDROLASE / metalloprotease | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Agrawal, R. / Kumar, A. / Kumar, A. / Makde, R.D. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2020 Title: Structural basis for the unusual substrate specificity of unique two-domain M1 metallopeptidase. Authors: Agrawal, R. / Goyal, V.D. / Singh, R. / Kumar, A. / 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 | 6kp1.cif.gz | 228.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kp1.ent.gz | 144.7 KB | Display | PDB format |
PDBx/mmJSON format | 6kp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/6kp1 ftp://data.pdbj.org/pub/pdb/validation_reports/kp/6kp1 | HTTPS FTP |
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-Related structure data
Related structure data | 6iffC 6koyC 6kozC 6kp0C 6a8zS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q9RVZ5 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 33.25 % / Description: Plate like crystals |
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Crystal grow | Temperature: 294 K / Method: microbatch / Details: Bis-tris, ammonium formate, PEG3350 / PH range: 5.5-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9778 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 18, 2018 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→47.5 Å / Num. obs: 36707 / % possible obs: 97.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.55 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.19→2.26 Å / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2953 / CC1/2: 0.956 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6A8Z Resolution: 2.19→21.45 Å / SU ML: 0.2724 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 29.727
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.19→21.45 Å
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Refine LS restraints |
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LS refinement shell |
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