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Yorodumi- PDB-2dgl: Crystal structure of Escherichia coli GadB in complex with bromide -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dgl | ||||||
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Title | Crystal structure of Escherichia coli GadB in complex with bromide | ||||||
Components | Glutamate decarboxylase beta | ||||||
Keywords | LYASE / GadB complexed with bromide | ||||||
Function / homology | Function and homology information glutamate decarboxylase / glutamate decarboxylase activity / glutamate catabolic process / intracellular pH elevation / pyridoxal phosphate binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | ||||||
Authors | Gruetter, M.G. / Capitani, G. / Gut, H. | ||||||
Citation | Journal: Embo J. / Year: 2006 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: Journal: Embo J. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dgl.cif.gz | 525.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dgl.ent.gz | 436.2 KB | Display | PDB format |
PDBx/mmJSON format | 2dgl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/2dgl ftp://data.pdbj.org/pub/pdb/validation_reports/dg/2dgl | HTTPS FTP |
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-Related structure data
Related structure data | 2dgkC 2dgmC 1pmmS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 52727.957 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Gene: gadB / Plasmid: PQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P69910, glutamate decarboxylase #2: Chemical | ChemComp-BR / #3: Chemical | ChemComp-PLP / #4: Chemical | ChemComp-ACY / #5: 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: 4.7 Å3/Da / Density % sol: 73.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% PEG 2000 MME, 0.18M potassium bromide, 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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 9, 2004 / 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: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→40 Å / Num. obs: 104068 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 39.4 Å2 / Rsym value: 0.129 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 3.15→3.26 Å / Mean I/σ(I) obs: 2.7 / Num. unique all: 10263 / Rsym value: 0.475 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1PMM Resolution: 3.15→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: 37.7 Å2 | ||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.15→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.15→3.26 Å
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