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Yorodumi- PDB-1ihd: Crystal Structure of Trigonal Form of D90E Mutant of Escherichia ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ihd | ||||||
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Title | Crystal Structure of Trigonal Form of D90E Mutant of Escherichia coli Asparaginase II | ||||||
Components | L-asparaginase IIAsparaginase | ||||||
Keywords | HYDROLASE / L-asparaginase / leukemia | ||||||
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: 2.65 Å | ||||||
Authors | Borek, D. / Jaskolski, M. | ||||||
Citation | Journal: Febs J. / Year: 2014 Title: Crystal structure of active site mutant of antileukemic L-asparaginase reveals conserved zinc-binding site. Authors: Borek, D. / Kozak, M. / Pei, J. / Jaskolski, M. #1: 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. #2: 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. #3: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2001 Title: Structures of Two Highly Homologous Bacterial L-Asparaginases: A Case of Enantiomorphic Space Groups Authors: Jaskolski, M. / Kozak, M. / Lubkowski, J. / Palm, G. / Wlodawer, A. #4: Journal: ACTA BIOCHIM.POL. / Year: 1997 Title: Why a "benign" Mutation Kills Enzyme Activity. Structure-based Analysis of the A176V Mutant of Saccharomyces cerevisiae L-asparaginase I Authors: Bonthron, D.T. / Jaskolski, M. #5: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 2000 Title: Dynamics of a Mobile Loop at the Active Site of Escherichia coli Asparaginase Authors: Aung, H.P. / Bocola, M. / Schleper, S. / Rohm, K.H. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE BIOLOGICALLY SIGNIFICANT OLIGOMER IS A HOMOTETRAMER WITH 222 SYMMETRY. THE ASYMMETRIC UNIT CONSIST OF MONOMERS A AND C WHICH FORM THE ACTIVE-SITE-COMPETENT DIMER WITH NON-CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY. THE COMPLETE TETRAMER IS GENERATED FROM THE AC DIMER THROUGH CRYSTALLOGRAPHIC TWO-FOLD ROTATION. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ihd.cif.gz | 123.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ihd.ent.gz | 96.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ihd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/1ihd ftp://data.pdbj.org/pub/pdb/validation_reports/ih/1ihd | HTTPS FTP |
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-Related structure data
Related structure data | 1jazC 1jjaC 3ecaS S: Starting model for refinement C: citing same article (ref.) |
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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 | The biological assembly is a homotetramer generated from the asymmetric-unit dimer by crystallographic two-fold rotation. |
-Components
#1: Protein | Mass: 34640.836 Da / Num. of mol.: 2 / Mutation: D90E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00805, asparaginase #2: Water | ChemComp-HOH / | |
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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: 2.7 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: sodium citrate, HEPES, PH 7.5, 292 K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.54178 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1998 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→20 Å / Num. all: 21080 / Num. obs: 21041 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 54.3 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 3 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.2 / % possible all: 96.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Active dimer (AC) from native L-asparaginase II structure - PDB code: 3ECA Resolution: 2.65→10 Å / SU B: 10.20916 / SU ML: 0.21554 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 1.01792 / ESU R Free: 0.27561 / Stereochemistry target values: Engh & Huber Details: Maximum likelihood algorithm. TLS parameters were used. RESIDUES 16-34 IN MOLECULE A AND RESIDUES 16-33 IN MOLECULE B NOT INCLUDED IN THE MODEL DUE TO POOR ELECTRON DENSITY.
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Displacement parameters | Biso mean: 19.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→10 Å
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Refine LS restraints |
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