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Yorodumi- PDB-1xey: Crystal structure of the complex of Escherichia coli GADA with gl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xey | ||||||
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Title | Crystal structure of the complex of Escherichia coli GADA with glutarate at 2.05 A resolution | ||||||
Components | Glutamate decarboxylase alpha | ||||||
Keywords | LYASE / GLUTAMATE DECARBOXYLASE / COMPLEX WITH GLUTARATE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Dutyshev, D.I. / Darii, E.L. / Fomenkova, N.P. / Pechik, I.V. / Polyakov, K.M. / Nikonov, S.V. / Andreeva, N.S. / Sukhareva, B.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structure of Escherichia coli glutamate decarboxylase (GADalpha) in complex with glutarate at 2.05 angstroms resolution. Authors: Dutyshev, D.I. / Darii, E.L. / Fomenkova, N.P. / Pechik, I.V. / Polyakov, K.M. / Nikonov, S.V. / Andreeva, N.S. / Sukhareva, B.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xey.cif.gz | 196.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xey.ent.gz | 156.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/1xey ftp://data.pdbj.org/pub/pdb/validation_reports/xe/1xey | HTTPS FTP |
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-Related structure data
Related structure data | 1pmmS S: Starting model for refinement |
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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: 52743.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GADA / Plasmid: PGAD1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P69908, glutamate decarboxylase #2: Chemical | #3: Chemical | #4: Chemical | #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: 2.58 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PYRIDINE CHLORIDE, GLYCEROL,SODIUM CHLORIDE, SODIUM ACETATE, PEG 3000, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-6 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 25, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→29.27 Å / Num. all: 60197 / Num. obs: 60197 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.091 / Net I/σ(I): 9.97 |
Reflection shell | Resolution: 2.05→2.1 Å / Mean I/σ(I) obs: 4.46 / Rsym value: 0.26 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PMM Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.085 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.183 / ESU R Free: 0.162 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.201 Å2
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Refine analyze | Luzzati coordinate error obs: 0.199 Å / Luzzati sigma a obs: 0.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20 /
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