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Open data
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Basic information
Entry | Database: PDB / ID: 4q0m | ||||||
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Title | Crystal structure of Pyrococcus furiosus L-asparaginase | ||||||
![]() | L-asparaginase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() asparaginase / asparaginase activity / amino acid metabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sharma, P. / Tomar, R. / Singh, S. / Yadav, S.P.S. / Ashish / Kundu, B. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80 KB | Display | ![]() |
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PDB format | ![]() | 58.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4njeC ![]() 4ra6C ![]() 4ra9C ![]() 4lx7 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
#1: Protein | Mass: 35933.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-PO4 / | ||||
#3: Chemical | #4: Chemical | ChemComp-4CS / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 200mM Ammonium dihydrogen phosphate, 100mM Tris, 50% MPD, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: Mar 28, 2014 / 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: 2.21→61.17 Å / Num. all: 19525 / Num. obs: 19525 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 23.58 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.21→2.33 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 5.2 / Num. unique all: 2388 / Rsym value: 0.435 / % possible all: 82.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4LX7 ![]() 4lx7 Resolution: 2.226→47.893 Å / FOM work R set: 0.777 / SU ML: 0.56 / σ(F): 1.33 / Phase error: 27.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.856 Å2 / ksol: 0.385 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.18 Å2 / Biso mean: 32.75 Å2 / Biso min: 13.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2.226→47.893 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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