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- PDB-2dgm: Crystal structure of Escherichia coli GadB in complex with iodide -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dgm | ||||||
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Title | Crystal structure of Escherichia coli GadB in complex with iodide | ||||||
![]() | Glutamate decarboxylase beta | ||||||
![]() | LYASE / GadB complexed with iodide | ||||||
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 | ![]() | 570 KB | Display | ![]() |
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PDB format | ![]() | 464.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 538.9 KB | Display | ![]() |
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Full document | ![]() | 580.9 KB | Display | |
Data in XML | ![]() | 117.9 KB | Display | |
Data in CIF | ![]() | 164.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dgkC ![]() 2dglC ![]() 1pmmS 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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Unit cell |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 52727.957 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 1976 molecules ![](data/chem/img/IOD.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-IOD / #3: Chemical | ChemComp-PLP / #4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-ACY / | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.135M sodium acetate, 0.7M sodium formate, 13% PEG 4000, pH 4.6, 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: May 2, 2003 / 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: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→40 Å / Num. obs: 191280 / % possible obs: 92.7 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Biso Wilson estimate: 20.9 Å2 / Rsym value: 0.12 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 17342 / Rsym value: 0.26 / % possible all: 84.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1PMM Resolution: 1.95→40 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: 21 Å2 | ||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å
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