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- PDB-1hfw: X-ray structure of the complex between Erwinia chrysanthemi L-asp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1hfw | ||||||
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Title | X-ray structure of the complex between Erwinia chrysanthemi L-asparaginase and L-Glutamate | ||||||
![]() | L-ASPARAGINASE | ||||||
![]() | ASPARAGINASE / HYDROLASE / COMPLEX / D-ASPARTATE | ||||||
Function / homology | ![]() asparagine metabolic process / asparaginase / asparaginase activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lubkowski, J. / Wlodawer, A. / Kolyani, K.A. | ||||||
![]() | ![]() Title: Stuctural Basis for the Activity and Substrate Specificity of Erwinia Chrysanthemi L-Asparaginase Authors: Kolyani, K.A. / Wlodawer, A. / Lubkowski, J. #1: Journal: FEBS Lett. / Year: 1993 Title: A Left-Handed Crossover Involved in Amidohydrolase Catalysis, Crystal Structure of Erwinia Chrysanthemi L-Asparaginase with Bound L-Aspartate Authors: Miller, M. / Rao, J.K.M. / Wlodawer, A. / Gribskov, M.R. #2: ![]() 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.M. / Wlodawer, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 255.4 KB | Display | ![]() |
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PDB format | ![]() | 208.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.6 KB | Display | ![]() |
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Full document | ![]() | 484.3 KB | Display | |
Data in XML | ![]() | 54.3 KB | Display | |
Data in CIF | ![]() | 79.1 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 | BIOLOGICAL_UNIT: HOMOTETRAMER |
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Components
#1: Protein | Mass: 35123.020 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: THE NEW NAME OF ERWINIA CHRYSANTHEMI IS PECTOBACTERIUM CHRYSANTHEMI Source: (natural) ![]() #2: Chemical | ChemComp-GLU / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.77 % | ||||||||||||||||||||
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Crystal grow | pH: 5.4 Details: 40%(W/V) AMMONIUM SULFATE, 2%(V/V) PEG400, 0.1M TRIS (PH 8.5), CROSSLINKING WITH 0.1% GLUTARALDEHYDE. TRANSFER TO AMMONIUM SULFATE-FREE, 30% PEG4000, CHANGE OF THE BUFFER TO 0.1M SODIUM ACETATE | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Miller, M., (1993) FEBS Lett., 328, 275. / PH range low: 9 / PH range high: 8 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 15, 1998 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5478 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 102023 / % possible obs: 86 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rsym value: 0.076 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.337 / % possible all: 65.4 |
Reflection | *PLUS Num. measured all: 270156 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 65.4 % / Rmerge(I) obs: 0.337 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PREVIUOSLY PUBLISHED STRUCTURE OF ERWINIA CHRYSANTHEMI L-ASPARAGINSE (MILLER ET AL., FEBS LETT., 1993 Resolution: 1.8→10 Å / Rfactor Rfree error: 0.0045 / Data cutoff high absF: 100000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: DENSITY MODIFICATION / Bsol: 84.82 Å2 / ksol: 0.421 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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