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- PDB-2gaw: WILD TYPE GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gaw | ||||||
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Title | WILD TYPE GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM | ||||||
![]() | (GLYCOSYLASPARAGINASE) x 2 | ||||||
![]() | HYDROLASE / GLYCOSYLASPARAGINASE / N-TERMINAL NUCLEOPHILE HYDROLASE / AUTOPROTEOLYSIS | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Guo, H.-C. / Xu, Q. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.2 KB | Display | ![]() |
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PDB format | ![]() | 89 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99998, 0.0057, -0.00245), 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. | |
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Components
#1: Protein | Mass: 16819.072 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PMAL FUSION PROTEIN / Production host: ![]() ![]() References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase #2: Protein | Mass: 15378.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PMAL FUSION PROTEIN / Production host: ![]() ![]() References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 32 % Description: INITIAL MODEL WAS FROM A PARTIAL T152C MUTANT MODEL BY MIR METHOD | ||||||||||||||||||||
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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: ![]() |
Detector | Type: RIGAKU RAXIS IIC / 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: 2.2 Å / Num. obs: 23999 / % possible obs: 86.7 % / Observed criterion σ(I): -2 / Redundancy: 1.76 % / Rsym value: 0.11 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 1.23 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.135 / % possible all: 63.3 |
Reflection | *PLUS Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 63.3 % / Rmerge(I) obs: 0.135 |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 10.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→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: 2.2→2.29 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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