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Yorodumi- PDB-3abq: Crystal structure of ethanolamine ammonia-lyase from Escherichia ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3abq | |||||||||
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Title | Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl and 2-amino-1-propanol | |||||||||
Components | (Ethanolamine ammonia-lyase ...) x 2 | |||||||||
Keywords | LYASE / (beta/alpha)8 fold / Cobalt / Cobalamin | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Shibata, N. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates. Authors: Shibata, N. / Tamagaki, H. / Hieda, N. / Akita, K. / Komori, H. / Shomura, Y. / Terawaki, S. / Mori, K. / Yasuoka, N. / Higuchi, Y. / Toraya, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3abq.cif.gz | 579.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3abq.ent.gz | 477.3 KB | Display | PDB format |
PDBx/mmJSON format | 3abq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3abq_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 3abq_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 3abq_validation.xml.gz | 64.1 KB | Display | |
Data in CIF | 3abq_validation.cif.gz | 91.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/3abq ftp://data.pdbj.org/pub/pdb/validation_reports/ab/3abq | HTTPS FTP |
-Related structure data
Related structure data | 3aboSC 3abrC 3absC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
-Ethanolamine ammonia-lyase ... , 2 types, 4 molecules ACBD
#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: b2441, eutB, JW2434 / Plasmid: pUSI2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0AEJ6, ethanolamine ammonia-lyase #2: Protein | Mass: 33197.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2440, eutC, JW2433 / Plasmid: pUSI2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P19636, ethanolamine ammonia-lyase |
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-Non-polymers , 4 types, 1022 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: 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: 3.9 Å3/Da / Density % sol: 68.44 % |
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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.M imidazole-HCl, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 5, 2009 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 158931 / Num. obs: 158931 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.55 / Num. unique all: 10007 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 3ABO Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.878 / SU B: 10.235 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 13.083 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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