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Yorodumi- PDB-5b74: Crystal structure of conjoined Pyrococcus furiosus L-asparaginase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b74 | ||||||
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Title | Crystal structure of conjoined Pyrococcus furiosus L-asparaginase with peptide | ||||||
Components |
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Keywords | HYDROLASE / Truncated Pyrococcus furiosus L-asparaginase / Linkerless | ||||||
Function / homology | Function and homology information asparaginase / asparaginase activity / amino acid metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus DSM 3638 (archaea) Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.039 Å | ||||||
Authors | Sharma, P. / Tomar, R. / Nath, S.K. / Kundu, B. / Ashish, F. | ||||||
Citation | Journal: Sci Rep / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b74.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b74.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 5b74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/5b74 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/5b74 | HTTPS FTP |
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-Related structure data
Related structure data | 5b5uC 5cbpC 4ra9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 19891.836 Da / Num. of mol.: 1 / Fragment: N-Terminal domain UNP residues 1-182 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Strain: DSM 3638 / Gene: PF2047 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8TZE8, asparaginase |
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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.) Pyrococcus furiosus DSM 3638 (archaea) / Strain: DSM 3638 / Gene: PF2047 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8TZE8, asparaginase |
-Protein/peptide , 1 types, 1 molecules D
#3: Protein/peptide | Mass: 443.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus furiosus (archaea) |
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-Non-polymers , 3 types, 106 molecules
#4: Chemical | ChemComp-FLC / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.15 % |
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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 PH range: 7.5-9.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 7, 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: 2.03→49.11 Å / Num. obs: 29314 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.03→2.14 Å / Redundancy: 13 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.4 / % possible all: 82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RA9 Resolution: 2.039→49.109 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.27
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 49.878 Å2 / ksol: 0.355 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.039→49.109 Å
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Refine LS restraints |
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LS refinement shell |
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