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- PDB-6f2f: Crystal structure of Protease 1 from Pyrococcus Horikoshii co-cys... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6f2f | ||||||
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Title | Crystal structure of Protease 1 from Pyrococcus Horikoshii co-cystallized in presence of 10 mM Tb-Xo4 and ammonium sulfate. | ||||||
![]() | Deglycase PH1704 | ||||||
![]() | CELL CYCLE / Lanthanide complexes / Tb-Xo4 / Crystallophore / Phasing / nucleation | ||||||
Function / homology | ![]() protein deglycase / protein deglycase activity / peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Engilberge, S. / Riobe, F. / Di Pietro, S. / Franzetti, B. / Girard, E. / Dumont, E. / Maury, O. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Unveiling the Binding Modes of the Crystallophore, a Terbium-based Nucleating and Phasing Molecular Agent for Protein Crystallography. Authors: Engilberge, S. / Riobe, F. / Wagner, T. / Di Pietro, S. / Breyton, C. / Franzetti, B. / Shima, S. / Girard, E. / Dumont, E. / Maury, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 412.1 KB | Display | ![]() |
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PDB format | ![]() | 341.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 40.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6f2hC ![]() 6f2iC ![]() 6f2jC ![]() 6f2kC ![]() 6f2mC ![]() 6frmC ![]() 6frnC ![]() 6froC ![]() 6frqC ![]() 1g2iS 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 4 molecules ABC![](data/chem/img/2HA.gif)
![](data/chem/img/2HA.gif)
#1: Protein | Mass: 18650.418 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O59413, protein deglycase, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #5: Sugar | ChemComp-2HA / | |
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-Non-polymers , 4 types, 626 molecules ![](data/chem/img/7MT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/TB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/TB.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-TB / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.9 to 2.4 ammonium sulfate, 0.2 M sodium potassium tartrate, 100 mM trisodium citrate dehydrate pH 5.6. 10 mM Tb-Xo4 were solubilized with the protein solution prior to perform crystallization drops. |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97974 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→44.77 Å / Num. obs: 121190 / % possible obs: 99.8 % / Redundancy: 11.5 % / Biso Wilson estimate: 25.59 Å2 / Rpim(I) all: 0.031 / Net I/σ(I): 14.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1G2I Resolution: 1.65→44.77 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.956 / SU R Cruickshank DPI: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.061 / SU Rfree Blow DPI: 0.058 / SU Rfree Cruickshank DPI: 0.055
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Displacement parameters | Biso mean: 29.54 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.65→44.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.69 Å / Total num. of bins used: 20
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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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