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Yorodumi- PDB-2oiz: Crystal Structure of the Tryptamine-Derived (Indol-3-Acetamide)-T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oiz | ||||||
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Title | Crystal Structure of the Tryptamine-Derived (Indol-3-Acetamide)-TTQ Adduct of Aromatic Amine Dehydrogenase | ||||||
Components |
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Keywords | OXIDOREDUCTASE / tryptophan tryptophyl quinone / H-tunneling | ||||||
Function / homology | Function and homology information aralkylamine dehydrogenase (azurin) / aralkylamine dehydrogenase (azurin) activity / aliphatic amine dehydrogenase activity / amine metabolic process / periplasmic space Similarity search - Function | ||||||
Biological species | Alcaligenes faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 Å | ||||||
Authors | Roujeinikova, A. / Leys, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: New insights into the reductive half-reaction mechanism of aromatic amine dehydrogenase revealed by reaction with carbinolamine substrates. Authors: Roujeinikova, A. / Hothi, P. / Masgrau, L. / Sutcliffe, M.J. / Scrutton, N.S. / Leys, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oiz.cif.gz | 453.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oiz.ent.gz | 367.3 KB | Display | PDB format |
PDBx/mmJSON format | 2oiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oiz_validation.pdf.gz | 484.8 KB | Display | wwPDB validaton report |
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Full document | 2oiz_full_validation.pdf.gz | 502.9 KB | Display | |
Data in XML | 2oiz_validation.xml.gz | 54.6 KB | Display | |
Data in CIF | 2oiz_validation.cif.gz | 86.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/2oiz ftp://data.pdbj.org/pub/pdb/validation_reports/oi/2oiz | HTTPS FTP |
-Related structure data
Related structure data | 2i0rC 2i0sC 2i0tC 2ojyC 2ok4C 2ok6C 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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Unit cell |
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Details | The asymmetric unit contains a biological heterotetramer |
-Components
#1: Protein | Mass: 14516.898 Da / Num. of mol.: 2 / Fragment: (Residues: 48-182) / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) References: UniProt: Q0VKG6, UniProt: P84887*PLUS, EC: 1.4.99.4 #2: Protein | Mass: 40016.125 Da / Num. of mol.: 2 / Fragment: (Residues: 73-433) / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) References: UniProt: Q0VKG7, UniProt: P84888*PLUS, EC: 1.4.99.4 #3: Chemical | #4: Chemical | ChemComp-PG4 / | #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: 2.31 Å3/Da / Density % sol: 46.83 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG 2000 MME, AMMONIUM SULPHATE, SODIUM CACODYLATE, TRYPTAMINE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Monochromator: TRIANGULAR HORIZONTAL- FOCUSING SI III MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.05→15 Å / Num. obs: 383635 / % possible obs: 83.6 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rmerge(I) obs: 0.064 / Χ2: 0.954 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.05→1.07 Å / Redundancy: 2 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 1.9 / Num. unique all: 16727 / Χ2: 1.056 / % possible all: 73 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.05→15 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.69 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 11.547 Å2
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Refinement step | Cycle: LAST / Resolution: 1.05→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.05→1.077 Å / Total num. of bins used: 20
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