+Open data
-Basic information
Entry | Database: PDB / ID: 1pmm | ||||||
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Title | Crystal structure of Escherichia coli GadB (low pH) | ||||||
Components | Glutamate decarboxylase beta | ||||||
Keywords | LYASE / LOW-PH FORM OF GadB | ||||||
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 / MAD / Resolution: 2 Å | ||||||
Authors | Capitani, G. / De Biase, D. / Aurizi, C. / Gut, H. / Bossa, F. / Grutter, M.G. | ||||||
Citation | 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. / Grutter, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pmm.cif.gz | 555.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pmm.ent.gz | 468 KB | Display | PDB format |
PDBx/mmJSON format | 1pmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/1pmm ftp://data.pdbj.org/pub/pdb/validation_reports/pm/1pmm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE BIOLOGICAL ASSEMBLY IS A HEXAMER |
-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) / Gene: GADB / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P69910, glutamate decarboxylase #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-ACY / #4: 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: 2.3 Å3/Da / Density % sol: 46.53 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: sodium formate, sodium acetate, PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9184 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 12, 2003 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2→24.62 Å / Num. obs: 178481 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 6.3 / Num. unique all: 17609 / % possible all: 94.6 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å |
Reflection shell | *PLUS Highest resolution: 2 Å / Mean I/σ(I) obs: 6.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NULL Resolution: 2→24.62 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: 15.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→24.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.03 Å
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 25 Å / Rfactor Rwork: 0.183 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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