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- PDB-2dgk: Crystal structure of an N-terminal deletion mutant of Escherichia... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dgk | ||||||
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Title | Crystal structure of an N-terminal deletion mutant of Escherichia coli GadB in an autoinhibited state (aldamine) | ||||||
![]() | Glutamate decarboxylase beta | ||||||
![]() | LYASE / GadB / GadBD1-14 / autoinhibition / substituted aldamine | ||||||
Function / homology | ![]() glutamate decarboxylase / glutamate decarboxylase activity / intracellular pH elevation / glutamate catabolic process / pyridoxal phosphate binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gruetter, M.G. / Capitani, G. / Gut, H. | ||||||
![]() | ![]() Title: Escherichia coli acid resistance: pH-sensing, activation by chloride and autoinhibition in GadB Authors: Gut, H. / Pennacchietti, E. / John, R.A. / Bossa, F. / Capitani, G. / De Biase, D. / Gruetter, M.G. #1: ![]() Title: Crystal structure and functional analysis of Escherichia coli glutamate decarboxylase Authors: Capitani, G. / De Biase, D. / Aurizi, C. / Gut, H. / Bossa, F. / Gruetter, M.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 547.7 KB | Display | ![]() |
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PDB format | ![]() | 449.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2dglC ![]() 2dgmC ![]() 1pmoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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6 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51067.016 Da / Num. of mol.: 6 / Fragment: GadBD1-14 / Mutation: deletion of 14 N-terminal residues Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PLP / #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 22.5% PEG 2000 MME, 0.18M litium sulfate, 0.1M sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 30, 2005 / Details: dynamically bendable mirror |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 230800 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.068 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.9→2.2 Å / Redundancy: 7 % / Mean I/σ(I) obs: 8.7 / Num. unique all: 81214 / Rsym value: 0.217 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1PMO Resolution: 1.9→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28.9 Å2 | ||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å
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