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Yorodumi- PDB-2agl: Crystal structure of the phenylhydrazine adduct of aromatic amine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2agl | ||||||
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Title | Crystal structure of the phenylhydrazine adduct of aromatic amine dehydrogenase from Alcaligenes faecalis | ||||||
Components | (Aromatic amine dehydrogenase) x 2 | ||||||
Keywords | OXIDOREDUCTASE | ||||||
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: 1.4 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 | 2agl.cif.gz | 219.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2agl.ent.gz | 171.8 KB | Display | PDB format |
PDBx/mmJSON format | 2agl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2agl_validation.pdf.gz | 469.1 KB | Display | wwPDB validaton report |
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Full document | 2agl_full_validation.pdf.gz | 476 KB | Display | |
Data in XML | 2agl_validation.xml.gz | 45.3 KB | Display | |
Data in CIF | 2agl_validation.cif.gz | 69.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/2agl ftp://data.pdbj.org/pub/pdb/validation_reports/ag/2agl | HTTPS FTP |
-Related structure data
Related structure data | 2agwC 2agxC 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: 46.8 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG 2000 MME, ammonium sulphate, sodium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Details: RADII TOROIDAL MIRROR |
Radiation | Monochromator: GE(220) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 187796 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.4→1.45 Å / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 4.1 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→15 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.969 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.062 / 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: 14.485 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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