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- PDB-5h0i: Structure of OaAEP1 asparaginyl peptide ligase in its proenzyme form -
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Open data
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Basic information
Entry | Database: PDB / ID: 5h0i | ||||||
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Title | Structure of OaAEP1 asparaginyl peptide ligase in its proenzyme form | ||||||
![]() | Asparaginyl endopeptidase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() legumain / proteolysis involved in protein catabolic process / cysteine-type endopeptidase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, R. / Wong, Y.H. / Lescar, J. / Wu, B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Engineering a Catalytically Efficient Recombinant Protein Ligase Authors: Yang, R. / Wong, Y.H. / Nguyen, G.K.T. / Tam, J.P. / Lescar, J. / Wu, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 331 KB | Display | ![]() |
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PDB format | ![]() | 268.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.3 KB | Display | ![]() |
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Full document | ![]() | 445.6 KB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 45.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nokS S: Starting model for refinement |
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Similar structure data |
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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: 49393.871 Da / Num. of mol.: 2 / Fragment: UNP residues 24-474 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.87 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 200mM NH4NO3, pH ~ 4.5, 13-15%(w/v) PEG 3,350 with 10%(v/v) glycerol or ethylene glycol |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→71.72 Å / Num. obs: 34420 / % possible obs: 99.7 % / Redundancy: 3 % / Biso Wilson estimate: 63.02 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.56→2.7 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.7 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4NOK Resolution: 2.56→71.72 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.901 / Rfactor Rfree error: 0.01 / SU R Cruickshank DPI: 0.419 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.427 / SU Rfree Blow DPI: 0.247 / SU Rfree Cruickshank DPI: 0.249
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Displacement parameters | Biso mean: 68.81 Å2
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Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.56→71.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.56→2.64 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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