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Yorodumi- PDB-1jsr: CRYSTAL STRUCTURE OF ERWINIA CHRYSANTHEMI L-ASPARAGINASE COMPLEXE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jsr | ||||||
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Title | CRYSTAL STRUCTURE OF ERWINIA CHRYSANTHEMI L-ASPARAGINASE COMPLEXED WITH 6-HYDROXY-L-NORLEUCINE | ||||||
Components | L-asparaginase | ||||||
Keywords | HYDROLASE / ASPARAGINASE / COVALENT COMPLEX / 6-DIAZO-5-OXO-L-NORLEUCINE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Erwinia chrysanthemi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / isomorphous replacement / Resolution: 1.7 Å | ||||||
Authors | Aghaiypour, K. / Wlodawer, A. / Lubkowski, J. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2001 Title: Do bacterial L-asparaginases utilize a catalytic triad Thr-Tyr-Glu? Authors: Aghaiypour, K. / Wlodawer, A. / Lubkowski, J. #1: Journal: Biochemistry / Year: 2001 Title: Structural Basis for the Activity and Substrate Specificity of Erwinia chrysanthemi L-Asparaginase Authors: Aghaiypour, K. / Wlodawer, A. / Lubkowski, J. #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. / Wlodawer, A. / Gribskov, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jsr.cif.gz | 280.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jsr.ent.gz | 226.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jsr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jsr_validation.pdf.gz | 484.1 KB | Display | wwPDB validaton report |
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Full document | 1jsr_full_validation.pdf.gz | 501.8 KB | Display | |
Data in XML | 1jsr_validation.xml.gz | 59.3 KB | Display | |
Data in CIF | 1jsr_validation.cif.gz | 86.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/1jsr ftp://data.pdbj.org/pub/pdb/validation_reports/js/1jsr | HTTPS FTP |
-Related structure data
Related structure data | 1jslC 1hg0S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Biologically relevant tetramer is present in the asymmetric unit |
-Components
#1: Protein | Mass: 35123.020 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / References: UniProt: P06608, asparaginase #2: Chemical | ChemComp-LDO / #3: Chemical | ChemComp-1PE / | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Nonpolymer details | 6-DIAZO-5-OXO-L-NORLEUCINE REACTS WITH THE ENZYME TO FORM A COVALENT COMPLEX BETWEEN THE ENZYME AND ...6-DIAZO-5-OXO-L-NORLEUCINE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.36 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: ammonium sulfate, PEG 400, TRIS buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Details: Miller, M., (1993) FEBS Lett., 328, 275. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 2000 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. all: 144902 / Num. obs: 135872 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.38 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.3 / Num. unique all: 8771 / Rsym value: 0.43 / % possible all: 91.1 |
Reflection | *PLUS Num. measured all: 323188 / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 91.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: isomorphous replacement Starting model: PDB CODE 1HG0 Resolution: 1.7→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 15.12 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.71 Å
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 1 / % reflection Rfree: 2 % / Rfactor all: 0.19 / Rfactor obs: 0.183 / Rfactor Rfree: 0.21 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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