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Yorodumi- PDB-1p4k: CRYSTAL STRUCTURE OF THE GLYCOSYLASPARAGINASE PRECURSOR D151N MUTANT -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p4k | ||||||
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Title | CRYSTAL STRUCTURE OF THE GLYCOSYLASPARAGINASE PRECURSOR D151N MUTANT | ||||||
Components | N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase | ||||||
Keywords | HYDROLASE / ALPHA BETA / BETA ALPHA / SANDWICH | ||||||
Function / homology | Function and homology information N4-(beta-N-acetylglucosaminyl)-L-asparaginase / N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity / peptidase activity / periplasmic space / proteolysis Similarity search - Function | ||||||
Biological species | Elizabethkingia meningoseptica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Qian, X. / Guan, C. / Guo, H.C. | ||||||
Citation | Journal: Structure / Year: 2003 Title: A dual role for an aspartic acid in glycosylasparaginase autoproteolysis. Authors: Qian, X. / Guan, C. / Guo, H.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p4k.cif.gz | 119.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p4k.ent.gz | 93.7 KB | Display | PDB format |
PDBx/mmJSON format | 1p4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/1p4k ftp://data.pdbj.org/pub/pdb/validation_reports/p4/1p4k | HTTPS FTP |
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-Related 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: 32178.645 Da / Num. of mol.: 2 / Fragment: Glycosylasparaginase, alpha and beta chains / Mutation: D151N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria) Plasmid: pMAL-c2X / Production host: Escherichia coli (E. coli) References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase #2: Chemical | ChemComp-GOL / |
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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: 2.26 Å3/Da / Density % sol: 45.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: evaporation / pH: 7.5 Details: 15% PEG 3300, 0.1M Tris, pH 7.5, 0.2M lithium sulfate, 0.1% sodium azide, EVAPORATION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 283 K / Method: sparse matrix sampling method / Details: Cui, T., (1999) Acta Crystallogr., D55, 1961. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 43851 / Num. obs: 43851 / Rsym value: 0.02 |
Reflection shell | Resolution: 1.9→1.97 Å / Rsym value: 0.04 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. obs: 43700 / % possible obs: 95.1 % / Num. measured all: 80492 / Rmerge(I) obs: 0.02 |
Reflection shell | *PLUS % possible obs: 95.2 % / Rmerge(I) obs: 0.04 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 13.2 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.2198 / Rfactor Rwork: 0.1819 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |