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Yorodumi- PDB-2gac: T152C MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gac | ||||||
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Title | T152C MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM | ||||||
Components | (GLYCOSYLASPARAGINASE) x 2 | ||||||
Keywords | HYDROLASE / GLYCOSYLASPARAGINASE / N-TERMINAL NUCLEOPHILE HYDROLASE / AUTOPROTEOLYSIS / MUTANT | ||||||
Function / homology | Function and homology information N4-(beta-N-acetylglucosaminyl)-L-asparaginase / N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity / asparaginase activity / beta-aspartyl-peptidase activity / periplasmic space / lysosome / proteolysis Similarity search - Function | ||||||
Biological species | Elizabethkingia meningoseptica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.1 Å | ||||||
Authors | Guo, H.-C. / Xu, Q. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Crystal structures of Flavobacterium glycosylasparaginase. An N-terminal nucleophile hydrolase activated by intramolecular proteolysis. Authors: Guo, H.C. / Xu, Q. / Buckley, D. / Guan, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gac.cif.gz | 117.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gac.ent.gz | 91.4 KB | Display | PDB format |
PDBx/mmJSON format | 2gac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gac_validation.pdf.gz | 451.8 KB | Display | wwPDB validaton report |
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Full document | 2gac_full_validation.pdf.gz | 464.8 KB | Display | |
Data in XML | 2gac_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 2gac_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/2gac ftp://data.pdbj.org/pub/pdb/validation_reports/ga/2gac | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99999, 0.00474, -0.00121), Vector: Details | THE ASYMMETRIC UNIT CONTAINS TWO MOLECULES OF HETERODIMERS (A+B AND C+D). EACH HETERODIMER IS AUTOPROTEOLYZED FROM A SINGLE CHAIN PRECURSOR THE SEQUENCE COMPARISON IS DONE. | |
-Components
#1: Protein | Mass: 16819.072 Da / Num. of mol.: 2 / Mutation: T152C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria) Plasmid: PMAL FUSION PROTEIN / Production host: Escherichia coli (E. coli) References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase #2: Protein | Mass: 15380.615 Da / Num. of mol.: 2 / Mutation: T152C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria) Plasmid: PMAL FUSION PROTEIN / Production host: Escherichia coli (E. coli) References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase #3: 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: 2.16 Å3/Da / Density % sol: 32 % | ||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1995 / Details: YALE MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.1 Å / Num. obs: 30530 / % possible obs: 96.2 % / Observed criterion σ(I): -2 / Redundancy: 1.93 % / Rsym value: 0.09 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 1.65 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.189 / % possible all: 77.8 |
Reflection | *PLUS % possible obs: 0.09 % / Num. measured all: 59059 |
Reflection shell | *PLUS % possible obs: 77.8 % / Rmerge(I) obs: 0.189 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.1→6 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED INDIVIDUAL B F / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 14.99 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→6 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.19 Å / Rfactor Rfree error: 0.02 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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