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Yorodumi- PDB-4eca: ASPARAGINASE FROM E. COLI, MUTANT T89V WITH COVALENTLY BOUND ASPARTATE -
+Open data
-Basic information
Entry | Database: PDB / ID: 4eca | |||||||||
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Title | ASPARAGINASE FROM E. COLI, MUTANT T89V WITH COVALENTLY BOUND ASPARTATE | |||||||||
Components | L-ASPARAGINE AMIDOHYDROLASEAsparaginase | |||||||||
Keywords | HYDROLASE / ACYL-ENZYME INTERMEDIATE / THREONINE AMIDOHYDROLASE | |||||||||
Function / homology | Function and homology information asparagine catabolic process / asparaginase / asparaginase activity / outer membrane-bounded periplasmic space / protein homotetramerization / periplasmic space / protein-containing complex / identical protein binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Palm, G.J. / Lubkowski, J. / Wlodawer, A. | |||||||||
Citation | Journal: FEBS Lett. / Year: 1996 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. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 3ECA |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4eca.cif.gz | 256.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eca.ent.gz | 211.8 KB | Display | PDB format |
PDBx/mmJSON format | 4eca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/4eca ftp://data.pdbj.org/pub/pdb/validation_reports/ec/4eca | HTTPS FTP |
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-Related structure data
Related structure data | 3ecaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 34739.926 Da / Num. of mol.: 4 / Mutation: T89V Source method: isolated from a genetically manipulated source Details: THR 12 IS ACYLATED BY ASPARTIC ACID IN EACH MONOMER Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cellular location: PERIPLASMATIC / Gene: ANSB / Plasmid: PTWE1 / Cellular location (production host): PERIPLASMATIC / Gene (production host): ANSB / Production host: Escherichia coli (E. coli) / Strain (production host): CU1783 / References: UniProt: P00805, asparaginase #2: Water | ChemComp-HOH / | Sequence details | RESIDUES 1 - 22 OF THE SEQUENCE IN UNIPROT ARE THE LEADER PEPTIDE. | |
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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: 3.74 Å3/Da / Density % sol: 65 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: CRYSTALS WERE GROWN BY VAPOR DIFFUSION PROTEIN SOLUTION: 17 MG/ML PROTEIN IN 10 MM TRIS-HCL, PH 7.0 WELL SOLUTION: 36% MPD, 100 MM SODIUM ASPARTATE, 100 MM SODIUM ACETATE, PH 5.0 DROP ...Details: CRYSTALS WERE GROWN BY VAPOR DIFFUSION PROTEIN SOLUTION: 17 MG/ML PROTEIN IN 10 MM TRIS-HCL, PH 7.0 WELL SOLUTION: 36% MPD, 100 MM SODIUM ASPARTATE, 100 MM SODIUM ACETATE, PH 5.0 DROP PROTEIN:WELL = 1:2 TEMPERATURE: 4C, vapor diffusion - hanging drop, temperature 277K PH range: 5.0-7.0 | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 8, 1995 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 68197 / % possible obs: 72 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.41 / % possible all: 58 |
Reflection | *PLUS Num. measured all: 197314 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ECA Resolution: 2.2→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Isotropic thermal model: INDIVIDUAL B-FACTORS / σ(F): 2.5 Details: THR 198 IS AN OUTLIER IN THE RAMACHANDRAN PLOT FOR ALL KNOWN ASPARAGINASE STRUCTURES.
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Displacement parameters | Biso mean: 20.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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