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Yorodumi- PDB-4pv3: Crystal structure of potassium-dependent plant-type L-asparaginas... -
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-Basic information
Entry | Database: PDB / ID: 4pv3 | ||||||
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Title | Crystal structure of potassium-dependent plant-type L-asparaginase from Phaseolus vulgaris in complex with Na+ cations | ||||||
Components |
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Keywords | HYDROLASE / metal binding sites / potassium coordination / K-dependent enzyme / Ntn-hydrolase / plant protein / L-asparaginase / isoaspartyl aminopeptidase / amidohydrolase | ||||||
Function / homology | (Glycosyl)asparaginase / Peptidase T2, asparaginase 2 / Asparaginase / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / hydrolase activity / Alpha Beta / Isoaspartyl peptidase/L-asparaginase 2 Function and homology information | ||||||
Biological species | Phaseolus vulgaris (French bean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Bejger, M. / Gilski, M. / Imiolczyk, B. / Jaskolski, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Na+/K+ exchange switches the catalytic apparatus of potassium-dependent plant L-asparaginase Authors: Bejger, M. / Imiolczyk, B. / Clavel, D. / Gilski, M. / Pajak, A. / Marsolais, F. / Jaskolski, M. #1: Journal: J.Mol.Biol. / Year: 2006 Title: Crystal structure of plant asparaginase Authors: Michalska, K. / Bujacz, G. / Jaskolski, M. #2: Journal: J.Biol.Chem. / Year: 2005 Title: Crystal structure of isoaspartyl aminopeptidase in complex with L-aspartate Authors: Michalska, K. / Brzezinski, K. / Jaskolski, M. #3: Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Crystal packing of plant-type L-asparaginase from Escherichia coli Authors: Michalska, K. / Borek, D. / Hernandez-Santoyo, A. / Jaskolski, M. #4: Journal: J.Biol.Chem. / Year: 2008 Title: The mechanism of autocatalytic activation of plant-type L-asparaginases Authors: Michalska, K. / Hernandez-Santoyo, A. / Jaskolski, M. #5: Journal: ACTA BIOCHIM.POL. / Year: 2006 Title: Structural aspects of L-asparaginases, their friends and relations Authors: Michalska, K. / Jaskolski, M. #6: Journal: Eur.J.Biochem. / Year: 2004 Title: Expression, purification and catalytic activity of Lupinus luteus asparagine -amidohydrolase and its Escherichia coli homolog Authors: Borek, D. / Michalska, K. / Brzezinski, K. / Kisiel, A. / Podkowi ski, J. / Bonthron, D.T. / Krowarsch, D. / Otlewski, J. / Jaskolski, M. #7: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization and preliminary crystallographic studies of a new L-asparaginase encoded by Escherichia coli genome Authors: Borek, D. / Jaskolski, M. #8: Journal: ACTA BIOCHIM.POL. / Year: 2001 Title: Sequence analysis of enzymes with asparaginase activity Authors: Borek, D. / Jaskolski, M. #9: Journal: Biochemistry / Year: 2012 Title: Structures of apo and product-bound human L-asparaginase: insights into the mechanism of autoproteolysis and substrate hydrolysis Authors: Nomme, J. / Su, Y. / Konrad, M. / Lavie, A. #10: Journal: Chem.Biol. / Year: 2013 Title: Free glicyne accelerates the autoproteolytic activation of human asparaginase Authors: Su, Y. / Karamitros, C.S. / Nomme, J. / McSorley, T. / Konrad, M. / Lavie, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pv3.cif.gz | 233.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pv3.ent.gz | 187.2 KB | Display | PDB format |
PDBx/mmJSON format | 4pv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pv3_validation.pdf.gz | 458 KB | Display | wwPDB validaton report |
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Full document | 4pv3_full_validation.pdf.gz | 465.2 KB | Display | |
Data in XML | 4pv3_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 4pv3_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/4pv3 ftp://data.pdbj.org/pub/pdb/validation_reports/pv/4pv3 | HTTPS FTP |
-Related structure data
Related structure data | 4pu6SC 4pv2C 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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-Components
#1: Protein | Mass: 21015.805 Da / Num. of mol.: 2 / Fragment: N-TERMINAL SUBUNIT ALPHA (UNP residues 1-195) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phaseolus vulgaris (French bean) / Gene: PHAVU_001G025000g / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: V7CU13, asparaginase #2: Protein | Mass: 13624.618 Da / Num. of mol.: 2 / Fragment: C-TERMINAL SUBUNIT BETA (UNP residues 196-326) Source method: isolated from a genetically manipulated source Details: SUBUNITS ALPHA (CHAINS A, C) AND BETA (CHAINS B, D) ARE, RESPECTIVELY, THE N- AND C-TERMINAL PRODUCTS OF AUTOPROTEOLYTIC CLEAVAGE OF A PRECURSOR Source: (gene. exp.) Phaseolus vulgaris (French bean) / Gene: PHAVU_001G025000g / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: V7CU13, asparaginase #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE DIFFERENCE | |
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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: 2.67 Å3/Da / Density % sol: 53.9 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% PEG3350, 0.1M bis tris propane, 0.2M sodium nitrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 14, 2012 |
Radiation | Monochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→46.55 Å / Num. all: 44381 / Num. obs: 44381 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 43.625 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 15.78 |
Reflection shell | Resolution: 2.09→2.21 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 2.47 / Num. unique all: 7009 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PU6 Resolution: 2.09→46.55 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.743 / SU ML: 0.127 / Isotropic thermal model: ISOTROPIC / Cross valid method: R free / ESU R: 0.159 / ESU R Free: 0.158 / Stereochemistry target values: Engh & Huber / Details: H ATOMS WERE ADDED AT RIDING POSITIONS
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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 mean: 37.988 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→46.55 Å
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