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- PDB-1jn9: Structure of Putative Asparaginase Encoded by Escherichia coli yb... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jn9 | ||||||
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Title | Structure of Putative Asparaginase Encoded by Escherichia coli ybiK Gene | ||||||
![]() | (PUTATIVE L-ASPARAGINASE) x 2 | ||||||
![]() | HYDROLASE / Ntn hydrolase / asparaginase / autoproteolysis | ||||||
Function / homology | ![]() beta-aspartyl-peptidase / asparagine catabolic process via L-aspartate / asparaginase activity / beta-aspartyl-peptidase activity / protein autoprocessing / hydrolase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Borek, D. / Jaskolski, M. | ||||||
![]() | ![]() Title: Crystal packing of plant-type L-asparaginase from Escherichia coli. Authors: Michalska, K. / Borek, D. / Hernandez-Santoyo, A. / Jaskolski, M. #1: ![]() Title: Crystallization and preliminary crystallographic studies of a new L-asparaginase encoded by the Escherichia coli genome Authors: Borek, D. / Jaskolski, M. #2: ![]() Title: A protein catalytic framework with an N-terminal nucleophile is capable of self-activation Authors: Brannigan, J.A. / Dodson, G. / Duggleby, H.J. / Moody, P.C. / Smith, J.L. / Tomchick, D.R. / Murzin, A.G. #3: ![]() Title: Crystal structure of glycosylasparaginase from Flavobacterium meningosepticum Authors: Xuan, J. / Tarentino, A.L. / Grimwood, B.G. / Plummer Jr., T.H. / Cui, T. / Guan, C. / Van Roey, P. #4: ![]() Title: Three-dimensional structure of human lysosomal aspartylglucosaminidase Authors: Oinonen, C. / Tikkanen, R. / Rouvinen, J. / Peltonen, L. #5: ![]() Title: Crystal structures of Flavobacterium glycosylasparaginase. An N-terminal nucleophile hydrolase activated by intramolecular proteolysis Authors: Guo, H.C. / Xu, Q. / Buckley, D. / Guan, C. #6: ![]() Title: Structural insights into the mechanism of intramolecular proteolysis Authors: Xu, Q. / Buckley, D. / Guan, C. / Guo, H.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.6 KB | Display | ![]() |
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PDB format | ![]() | 96.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.5 KB | Display | ![]() |
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Full document | ![]() | 456.4 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 35.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The polypeptide chain encoded by the cDNA undergoes autoproteolytic cleavage into two subunits, alpha and beta. The biological assembly is a heterotetramer (or a dimer of heterodimers) consisting of two subunits alpha and two subunits beta, (alpha,beta)2. |
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Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 18958.693 Da / Num. of mol.: 2 / Fragment: N-terminus (residues 2-178) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 14428.146 Da / Num. of mol.: 2 / Fragment: C-terminus (residues 179-321) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 243 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.39 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Tris HCl pH 8.5, 0.2 M calcium chloride, PEG 4000, PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 273K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-2 / Detector: CCD / Date: Aug 22, 2000 |
Radiation | Monochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→60 Å / Num. obs: 29401 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.27→2.31 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 5.3 / % possible all: 95.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: structure of a different crystal form available in the laboratory Resolution: 2.3→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25341 / Stereochemistry target values: Engh & Huber Details: TLS parameters were used. In each subunit, several C-terminal residues were not modeled due to poor electron density (160-178 in chain A, 313-321 in chain B, 159-178 in chain C, 314-321 in ...Details: TLS parameters were used. In each subunit, several C-terminal residues were not modeled due to poor electron density (160-178 in chain A, 313-321 in chain B, 159-178 in chain C, 314-321 in chain D). It is possible that (some of) the missing residues in subunits alpha (chains A,C) are absent because of proteolytic excision or degradation. THE N-TERMINAL MET 1 RESIDUES OF SUBUNITS ALPHA (CHAINS A AND C) ARE NOT PRESENT IN THE MATURE PROTEIN.
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Displacement parameters | Biso mean: 15.186 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |