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- PDB-6koy: Crystal structure of two domain M1 Zinc metallopeptidase E323A mu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6koy | ||||||
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Title | Crystal structure of two domain M1 Zinc metallopeptidase E323A mutant bound to L-tryptophan amino acid | ||||||
![]() | Zinc metalloprotease | ||||||
![]() | HYDROLASE / Metalloprotease | ||||||
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: 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 223.9 KB | Display | ![]() |
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PDB format | ![]() | 142.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 48.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6iffC ![]() 6kozC ![]() 6kp0C ![]() 6kp1C ![]() 6a8zS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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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 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.85 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: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 7, 2018 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→44.89 Å / Num. obs: 29930 / % possible obs: 97.5 % / Redundancy: 2.6 % / Biso Wilson estimate: 24.45 Å2 / CC1/2: 0.996 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.35→2.43 Å / Mean I/σ(I) obs: 4.1 / Num. unique obs: 2663 / CC1/2: 0.945 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6a8z Resolution: 2.35→41.91 Å / SU ML: 0.2821 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.7301
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→41.91 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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