[English] 日本語
Yorodumi- PDB-3any: Crystal structure of ethanolamine ammonia-lyase from escherichia ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3any | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ethanolamine ammonia-lyase from escherichia coli complexed with CN-CBL and (R)-2-amino-1-propanol | ||||||
Components |
| ||||||
Keywords | LYASE / (BETA/ALPHA)8 FOLD / COBALT / COBALAMIN / Tim Barrel | ||||||
Function / homology | Function and homology information ethanolamine ammonia-lyase / ethanolamine ammonia-lyase activity / ethanolamine ammonia-lyase complex / ethanolamine degradation polyhedral organelle / ethanolamine catabolic process / cobalamin binding / amino acid metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Shibata, N. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: How coenzyme B12-dependent ethanolamine ammonia-lyase deals with both enantiomers of 2-amino-1-propanol as substrates: structure-based rationalization. Authors: Shibata, N. / Higuchi, Y. / Toraya, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3any.cif.gz | 562.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3any.ent.gz | 466.9 KB | Display | PDB format |
PDBx/mmJSON format | 3any.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3any_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3any_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3any_validation.xml.gz | 58 KB | Display | |
Data in CIF | 3any_validation.cif.gz | 82 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/3any ftp://data.pdbj.org/pub/pdb/validation_reports/an/3any | HTTPS FTP |
-Related structure data
Related structure data | 3ao0C 3abrS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
|
-Components
#1: Protein | Mass: 49447.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: eutB, b2441, JW2434 / Plasmid: PUSI2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0AEJ6, ethanolamine ammonia-lyase #2: Protein | Mass: 28769.021 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 44-295 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: eutC, b2440, JW2433 / Plasmid: PUSI2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P19636, ethanolamine ammonia-lyase #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.23 Å3/Da / Density % sol: 70.93 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 6.0-7.0% (W/V) PEG 4000, 24-26 % (V/V), GLYCEROL, 1.0% (V/V) 2-METHYL-2,4-PENTANEDIOL (MPD), 0.1M IMIDAZOLE-HCL , pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 |
Detector | Type: BRUCKER DIP-6040 / Detector: IMAGE PLATE / Date: Jun 5, 2008 / Details: MIRRORS |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48 Å / Num. all: 141897 / Num. obs: 141897 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.99 / % possible all: 91.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3ABR Resolution: 2.1→47.84 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.883 / SU B: 12.178 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.579 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→47.84 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.099→2.154 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|