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- PDB-1hfj: Asparaginase from Erwinia chrysanthemi, hexagonal form with sulfate -
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Open data
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Basic information
Entry | Database: PDB / ID: 1hfj | ||||||
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Title | Asparaginase from Erwinia chrysanthemi, hexagonal form with sulfate | ||||||
![]() | L-ASPARAGINE AMIDOHYDROLASE | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() asparagine metabolic process / asparaginase / asparaginase activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Palm, G.J. / Lubkowski, J. / Kozak, M. / Jaskolski, M. / Wlodawer, A. | ||||||
![]() | ![]() Title: Structures of Two Highly Homologous Bacterial L-Asparaginases: A Case of Enantiomorphic Space Groups Authors: Jaskolski, M. / Kozak, M. / Lubkowski, J. / Palm, G.J. / Wlodawer, A. #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.M. / Wlodawer, A. #2: 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.4 KB | Display | ![]() |
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PDB format | ![]() | 112.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446 KB | Display | ![]() |
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Full document | ![]() | 454.2 KB | Display | |
Data in XML | ![]() | 30.1 KB | Display | |
Data in CIF | ![]() | 44.8 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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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.992362, -0.013099, -0.12266), Vector: Details | IN THE TETRAMER TWO ACTIVE SITES ARE FORMED BY EACH INTIMATE DIMER AC AND ITS CRYSTALLOGRAPHIC SYMMETRY MATE | |
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Components
#1: Protein | Mass: 35123.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THE NEW NAME OF ERWINIA CHRYSANTHEMI IS PECTOBACTERIUM CHRYSANTHEMI. Source: (natural) ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | RESIDUES 1 TO 21 IN THE DATABASE ENTRY CONSTITUTE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: HANGING DROP. PROTEIN SOLUTION: 35 MG/ML PROTEIN, 0.1 M CHES PH 8.5. WELL SOLUTION: 47% AMMONIUM SULFATE, 2% PEG 400 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 4.8 / Method: vapor diffusion / Details: Kozak, M., (2000) Acta Biochim. Pol., 47, 807. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: R-AXIS II / Detector: IMAGE PLATE / Date: Sep 15, 1995 |
Radiation | Monochromator: NI FILTER, 0.00025MM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 29191 / % possible obs: 84.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 18.4 Å2 / Rsym value: 0.105 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.4→2.55 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.28 / % possible all: 66.8 |
Reflection | *PLUS Num. measured all: 89335 / Rmerge(I) obs: 0.105 |
Reflection shell | *PLUS % possible obs: 66.8 % / Rmerge(I) obs: 0.28 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: FROM REFERENCE 3 Resolution: 2.4→10 Å / Rfactor Rfree error: 0.0059 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Stereochemistry target values: MLF (MAXIMUM LIKELYHOOD ON F'S)
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.35 Å2
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Refine analyze | Luzzati d res low obs: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev Biso : 0 Å2 / Rms dev position: 0 Å / Weight Biso : 0 / Weight position: 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.43 Å / Total num. of bins used: 27 /
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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