[English] 日本語
Yorodumi- PDB-2hj4: Crystal structure of Alcaligenes faecalis AADH complex with p-nit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hj4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Alcaligenes faecalis AADH complex with p-nitrobenzylamine | ||||||
Components |
| ||||||
Keywords | OXIDOREDUCTASE / kinetic isotope effect / p-substituted benzylamines | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Roujeinikova, A. / Leys, D. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Isotope effects reveal that para-substituted benzylamines are poor reactivity probes of the quinoprotein mechanism for aromatic amine dehydrogenase. Authors: Hothi, P. / Roujeinikova, A. / Khadra, K.A. / Lee, M. / Cullis, P. / Leys, D. / Scrutton, N.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2hj4.cif.gz | 218.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2hj4.ent.gz | 178.7 KB | Display | PDB format |
PDBx/mmJSON format | 2hj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/2hj4 ftp://data.pdbj.org/pub/pdb/validation_reports/hj/2hj4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2hjbC 2q7qC 2hj7 C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The asymmetric unit contains the biological unit, (alpha)2(beta)2 tetramer |
-Components
#1: Protein | Mass: 14516.898 Da / Num. of mol.: 2 / Fragment: AADH (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: AADH (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 | ChemComp-PNZ / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.49 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG 2000 MME, AMMONIUM SULPHATE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. obs: 99178 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.673 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 21.033 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
|