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- PDB-7v9o: Crystal structure of the lanthipeptide zinc-metallopeptidase EryP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7v9o | ||||||
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Title | Crystal structure of the lanthipeptide zinc-metallopeptidase EryP mutant E802R from saccharopolyspora erythraea | ||||||
![]() | Alanine aminopeptidase | ||||||
![]() | HYDROLASE / Aminopeptidase / Alanine aminopeptidase / CYTOSOLIC PROTEIN | ||||||
Function / homology | ![]() membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / peptide binding / proteolysis / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhao, C. / Zhao, N.L. / Bao, R. | ||||||
Funding support | 1items
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![]() | ![]() Title: Conformational remodeling enhances activity of lanthipeptide zinc-metallopeptidases. Authors: Zhao, C. / Sheng, W. / Wang, Y. / Zheng, J. / Xie, X. / Liang, Y. / Wei, W. / Bao, R. / Wang, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 393.4 KB | Display | ![]() |
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PDB format | ![]() | 315.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7v9nSC ![]() 7v9pC ![]() 7v9qC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 98262.562 Da / Num. of mol.: 1 / Mutation: E802R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338 Gene: SACE_1339, A8924_1736 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MES / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.05 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 20%(w/v), PEG 6000, MES 6.0, 200mM Ammonium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.77→19.86 Å / Num. obs: 88457 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.032 / Rrim(I) all: 0.085 / Net I/σ(I): 16.1 / Num. measured all: 597759 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7V9N Resolution: 1.77→19.57 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.53 Å2 / Biso mean: 16.633 Å2 / Biso min: 8.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.77→19.57 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: -25.558 Å / Origin y: -23.8583 Å / Origin z: 76.3137 Å
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Refinement TLS group |
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