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Yorodumi- PDB-3eca: CRYSTAL STRUCTURE OF ESCHERICHIA COLI L-ASPARAGINASE, AN ENZYME U... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eca | |||||||||
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Title | CRYSTAL STRUCTURE OF ESCHERICHIA COLI L-ASPARAGINASE, AN ENZYME USED IN CANCER THERAPY (ELSPAR) | |||||||||
Components | L-asparaginase 2 | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information asparagine catabolic process / asparagine metabolic 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 | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.4 Å | |||||||||
Authors | Swain, A.L. / Jaskolski, M. / Housset, D. / Rao, J.K.M. / Wlodawer, A. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 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. #1: Journal: J.Biol.Chem. / Year: 1988 Title: Preliminary Crystal Structure of Acinetobacter Glutaminasificans Glutaminase-Asparaginase Authors: Ammon, H.L. / Weber, I.T. / Wlodawer, A. / Harrison, R.W. / Gilliland, G.L. / Murphy, K.C. / Sjolin, L. / Roberts, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eca.cif.gz | 253.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eca.ent.gz | 210.9 KB | Display | PDB format |
PDBx/mmJSON format | 3eca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eca_validation.pdf.gz | 452.8 KB | Display | wwPDB validaton report |
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Full document | 3eca_full_validation.pdf.gz | 469.3 KB | Display | |
Data in XML | 3eca_validation.xml.gz | 50.4 KB | Display | |
Data in CIF | 3eca_validation.cif.gz | 72 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/3eca ftp://data.pdbj.org/pub/pdb/validation_reports/ec/3eca | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34626.766 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: The structure was determined for the clinical drug Elspar. The amino acid sequence differed in four places from the sequence of the K12 strain of E. coli asparaginase (V27A, N64D, S252T, T263N). Source: (natural) Escherichia coli (E. coli) / Plasmid details: Commercial drug References: UniProt: A0A377K0N3, UniProt: P00805*PLUS, asparaginase #2: Chemical | ChemComp-ASP / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.13 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M sodium acetate, MPD, PEG3350 | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR590 / Wavelength: 1.542 Å |
Detector | Type: SIEMENS-XENTRONICS / Detector: AREA DETECTOR / Date: Jan 1, 1992 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→10 Å / % possible obs: 85.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.055 |
Reflection | *PLUS Highest resolution: 2.3 Å / % possible obs: 74 % / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS Redundancy: 5.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.4→9.99 Å / Cor.coef. Fo:Fc: 0.974 / SU B: 3.053 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS ADDED IN RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 169.82 Å2 / Biso mean: 25.809 Å2 / Biso min: 2.86 Å2
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Refinement step | Cycle: final / Resolution: 2.4→9.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.458 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Rfactor obs: 0.149 / Num. reflection obs: 56390 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 0.054 |