+Open data
-Basic information
Entry | Database: PDB / ID: 6enz | ||||||
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Title | Crystal structure of mouse GADL1 | ||||||
Components | Acidic amino acid decarboxylase GADL1 | ||||||
Keywords | LYASE / decarboxylase / homodimer / pyridoxal phosphate | ||||||
Function / homology | Function and homology information sulfinoalanine decarboxylase / sulfinoalanine decarboxylase activity / Aspartate and asparagine metabolism / Degradation of cysteine and homocysteine / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / carboxy-lyase activity / carboxylic acid metabolic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Raasakka, A. / Mahootchi, E. / Winge, I. / Luan, W. / Kursula, P. / Haavik, J. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018 Title: Structure of the mouse acidic amino acid decarboxylase GADL1. Authors: Raasakka, A. / Mahootchi, E. / Winge, I. / Luan, W. / Kursula, P. / Haavik, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6enz.cif.gz | 368.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6enz.ent.gz | 306.5 KB | Display | PDB format |
PDBx/mmJSON format | 6enz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/6enz ftp://data.pdbj.org/pub/pdb/validation_reports/en/6enz | HTTPS FTP |
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-Related structure data
Related structure data | 2jisS 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: 60453.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gadl1 / Production host: Escherichia coli (E. coli) / References: UniProt: E9QP13, UniProt: Q80WP8*PLUS #2: Chemical | |
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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: 2.83 Å3/Da / Density % sol: 56.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 80 mM Na-cacodylate, pH 6.0, 14% PEG 8000, 160 mM Ca-acetate, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 25036 / % possible obs: 99.4 % / Redundancy: 6.4 % / Rrim(I) all: 0.328 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 3→3.08 Å / Redundancy: 6 % / Rrim(I) all: 3.535 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JIS Resolution: 3→42.184 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→42.184 Å
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