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- PDB-5b5u: Crystal structure of truncated Pyrococcus furiosus L-asparaginase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5b5u | ||||||
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Title | Crystal structure of truncated Pyrococcus furiosus L-asparaginase with peptide | ||||||
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![]() | HYDROLASE / Truncated Pyrococcus furiosus L-asparaginase / Linkerless | ||||||
Function / homology | ![]() asparaginase / asparaginase activity / amino acid metabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sharma, P. / Tomar, R. / Nath, S.K. / Kundu, B. / Ashish, F. | ||||||
![]() | ![]() Title: Heat induces end to end repetitive association in P. furiosus L-asparaginase which enables its thermophilic property. Authors: Sharma, P. / Tomar, R. / Yadav, S.S. / Badmalia, M.D. / Nath, S.K. / Kundu, 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 | ![]() | 75.1 KB | Display | ![]() |
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PDB format | ![]() | 54.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5b74C ![]() 5cbpC ![]() 4ra9S 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 , 2 types, 2 molecules AB
#1: Protein | Mass: 19466.314 Da / Num. of mol.: 1 / Fragment: N-Terminal domain UNP residues 1-178 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 13904.347 Da / Num. of mol.: 1 / Fragment: C-Terminal domain UNP residues 202-326 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein/peptide , 1 types, 2 molecules CE
#3: Protein/peptide | Mass: 443.537 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Non-polymers , 5 types, 35 molecules ![](data/chem/img/ASP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ASP / | ||||||
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#5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M Sodium citrate tribasic dihydrate, 0.1 M Sodium cacodylate 6, 30%(v/v) 2-Propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 4, 2016 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.61→72.83 Å / Num. obs: 13346 / % possible obs: 90.9 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 12.7 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.61→2.75 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 5.7 / % possible all: 88.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4RA9 Resolution: 2.61→60.374 Å / SU ML: 0.82 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.02 Å2 / ksol: 0.369 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.61→60.374 Å
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Refine LS restraints |
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LS refinement shell |
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