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- PDB-1jja: CRYSTAL STRUCTURE OF ORTHORHOMBIC FORM OF D90E MUTANT OF ESCHERIC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jja | ||||||
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Title | CRYSTAL STRUCTURE OF ORTHORHOMBIC FORM OF D90E MUTANT OF ESCHERICHIA COLI L-ASPARAGINASE II | ||||||
![]() | L-ASPARAGINASE II | ||||||
![]() | HYDROLASE / L-ASPARAGINASE / LEUKEMIA | ||||||
Function / homology | ![]() asparagine catabolic process / asparaginase / asparaginase activity / outer membrane-bounded periplasmic space / protein homotetramerization / periplasmic space / protein-containing complex / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Borek, D. / Kozak, M. / Jaskolski, M. | ||||||
![]() | ![]() Title: Crystal structure of active site mutant of antileukemic L-asparaginase reveals conserved zinc-binding site. Authors: Borek, D. / Kozak, M. / Pei, J. / Jaskolski, M. #1: ![]() Title: Crystal Structure of Escherichia coli L-asparaginase, An Enzyme Used in Cancer Therapy Authors: Swain, A.L. / Jaskolski, M. / Housset, D. / Rao, J.K. / Wlodawer, A. #2: ![]() Title: A Covalently Bound Catalytic Intermediate in Escherichia coli Asparaginase: Crystal Structure of a Thr-89-Val Mutant Authors: Palm, G.J. / Lubkowski, J. / Derst, C. / Schleper, S. / Rohm, K.H. / Wlodawer, A. #3: ![]() Title: Structures of Two Highly Homologous Bacterial L-Asparaginases: A Case of Enantiomorphic Space Groups Authors: Jaskolski, M. / Kozak, M. / Lubkowski, J. / Palm, G. / Wlodawer, A. #4: ![]() Title: Why a "benign" Mutation Kills Enzyme Activity. Structure-based Analysis of the A176V Mutant of Saccharomyces cerevisiae L-asparaginase I Authors: Bonthron, D.T. / Jaskolski, M. #5: ![]() Title: Dynamics of a Mobile Loop at the Active Site of Escherichia coli Asparaginase Authors: Aung, H.P. / Bocola, M. / Schleper, S. / Rohm, K.H. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAINS, A, B, C, D, E, F. THE BIOLOGICAL ASSEMBLY IS A HOMOTETRAMER. CHAINS A, B, C, D FORM ONE INDEPENDENT TETRAMER WITH NON-CRYSTALLOGRAPHIC 222 SYMMETRY. CHAINS E AND F FORM AN ACTIVE-SITE-COMPETENT DIMER (CORRESPONDING TO DIMER AC IN THE ABCD TETRAMER). THE COMPLETE EFE'F' TETRAMER IS GENERATED THROUGH THE CRYSTALLOGRAPHIC TWO-FOLD ROTATION. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 355.7 KB | Display | ![]() |
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PDB format | ![]() | 291.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.3 KB | Display | ![]() |
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Full document | ![]() | 513 KB | Display | |
Data in XML | ![]() | 70 KB | Display | |
Data in CIF | ![]() | 97.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ihdC ![]() 1jazC ![]() 3ecaS C: citing same article ( S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Details | The biological assembly is a homotetramer. The asymmetric unit contains six protein chains, A, B, C, D, E, F. Chains A, B, C, D form one independent tetramer with non-crystallographic 222 symmetry. Chains E and F form an active-site-competent dimer (corresponding to dimer AC in the ABCD tetramer). The complete EFE'F' tetramer is generated through the crystallographic two-fold rotation. |
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Components
#1: Protein | Mass: 34640.836 Da / Num. of mol.: 6 / Mutation: D90E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG MME550, bicine, NaCl , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 10, 1998 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. all: 75961 / Num. obs: 75961 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.14 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.3→2.41 Å / Redundancy: 3.07 % / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 1.8 / % possible all: 93.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Active dimer of native E.coli asparaginase II (PDB code: 3ECA) Resolution: 2.3→10 Å / SU B: 5.781 / SU ML: 0.136 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.40726 / ESU R Free: 0 Details: MAXIMUM LIKELIHOOD METHOD. RESIDUES 17-33 IN MONOMER A, 16-37 IN MONOMER B, 16-34 IN MONOMER D, 16-34 IN MONOMER E, 19-20 AND 30-33 IN MONOMER F ARE NOT PRESENT IN THE MODEL. IN MONOMER C, ...Details: MAXIMUM LIKELIHOOD METHOD. RESIDUES 17-33 IN MONOMER A, 16-37 IN MONOMER B, 16-34 IN MONOMER D, 16-34 IN MONOMER E, 19-20 AND 30-33 IN MONOMER F ARE NOT PRESENT IN THE MODEL. IN MONOMER C, THE COMPLETE FLEXIBLE LOOP BETWEEN RESIDUES 10 AND 40 HAS BEEN MODELED IN VERY GOOD ELECTRON DENSITY IN AN OPEN CONFORMATION.
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Displacement parameters | Biso mean: 39.399 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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