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Yorodumi- PDB-4ra6: Crystal structure of linker less Pyrococcus furiosus L-asparaginase -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ra6 | ||||||
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Title | Crystal structure of linker less Pyrococcus furiosus L-asparaginase | ||||||
Components | (L-asparaginaseAsparaginase) x 2 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information asparaginase / asparaginase activity / amino acid metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus DSM 3638 (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.503 Å | ||||||
Authors | Sharma, P. / Tomar, R. / Ashish / Kundu, B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structural and functional insights into an archaeal L-asparaginase obtained through the linker-less assembly of constituent domains. Authors: Tomar, R. / Sharma, P. / Srivastava, A. / Bansal, S. / Kundu, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ra6.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ra6.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ra6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/4ra6 ftp://data.pdbj.org/pub/pdb/validation_reports/ra/4ra6 | HTTPS FTP |
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-Related structure data
Related structure data | 4njeC 4q0mC 4ra9C 1wlsS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22265.480 Da / Num. of mol.: 2 / Fragment: UNP residues 1-182 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: PF2047, ph0066 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8TZE8, asparaginase #2: Protein | Mass: 16075.715 Da / Num. of mol.: 2 / Fragment: UNP residues 202-326 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: PF2047, ph0066 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8TZE8, asparaginase #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15%(v/v) Reagent akcohol, 100mM Imidazole/HCl, 200mM MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 25, 2013 / 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: 2.5→50 Å / Num. obs: 19946 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 44.52 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.53 / Num. unique all: 778 / Rsym value: 0.762 / % possible all: 76.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WLS Resolution: 2.503→37.945 Å / FOM work R set: 0.7734 / SU ML: 0.38 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 29.5 / 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: 61.502 Å2 / ksol: 0.368 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.45 Å2 / Biso mean: 50.94 Å2 / Biso min: 27.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.503→37.945 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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