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Yorodumi- PDB-2agx: Crystal structure of the Schiff base intermediate in the reductiv... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2agx | ||||||
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Title | Crystal structure of the Schiff base intermediate in the reductive half-reaction of aromatic amine dehydrogenase (AADH) with tryptamine. P212121 form | ||||||
Components | (Aromatic amine dehydrogenaseAralkylamine dehydrogenase (azurin)) x 2 | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information aralkylamine dehydrogenase (azurin) / aralkylamine dehydrogenase (azurin) activity / amine dehydrogenase activity / amine metabolic process / periplasmic space Similarity search - Function | ||||||
Biological species | Alcaligenes faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Masgrau, L. / Roujeinikova, A. / Johannissen, L.O. / Hothi, P. / Basran, J. / Ranaghan, K.E. / Mulholland, A.J. / Sutcliffe, M.J. / Scrutton, N.S. / Leys, D. | ||||||
Citation | Journal: Science / Year: 2006 Title: Atomic description of an enzyme reaction dominated by proton tunneling Authors: Masgrau, L. / Roujeinikova, A. / Johannissen, L.O. / Hothi, P. / Basran, J. / Ranaghan, K.E. / Mulholland, A.J. / 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 | 2agx.cif.gz | 205.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2agx.ent.gz | 162.2 KB | Display | PDB format |
PDBx/mmJSON format | 2agx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/2agx ftp://data.pdbj.org/pub/pdb/validation_reports/ag/2agx | HTTPS FTP |
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-Related structure data
Related structure data | 2aglC 2agwC 2agyC 2agzC 2ah0C 2ah1C 2agu 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 the biological unit (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) / Strain: IFO 14479 / References: UniProt: P84887, 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) / Strain: IFO 14479 / References: UniProt: P84888, EC: 1.4.99.4 #3: Chemical | #4: 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: 2.4 Å3/Da / Density % sol: 48.7 % |
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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 / Wavelength: 0.8 Å |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 49153 / % possible obs: 91 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 28 / % possible all: 75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: substrate-free AADH coordinates Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.26 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.268 / ESU R Free: 0.214 / 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: 22.518 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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