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Yorodumi- PDB-2iup: CRYSTAL STRUCTURE OF DITHIONITE-REDUCED AROMATIC AMINE DEHYDROGEN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iup | ||||||
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Title | CRYSTAL STRUCTURE OF DITHIONITE-REDUCED AROMATIC AMINE DEHYDROGENASE (AADH) FROM ALCALIGENES FAECALIS | ||||||
Components |
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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 / OTHER / Resolution: 1.8 Å | ||||||
Authors | Roujeinikova, A. / Scrutton, N. / Leys, D. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2006 Title: Atomic level insight into the oxidative half-reaction of aromatic amine dehydrogenase. Authors: Roujeinikova, A. / Scrutton, N.S. / Leys, D. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iup.cif.gz | 213.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iup.ent.gz | 177 KB | Display | PDB format |
PDBx/mmJSON format | 2iup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2iup_validation.pdf.gz | 456 KB | Display | wwPDB validaton report |
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Full document | 2iup_full_validation.pdf.gz | 466.6 KB | Display | |
Data in XML | 2iup_validation.xml.gz | 48.6 KB | Display | |
Data in CIF | 2iup_validation.cif.gz | 73.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/2iup ftp://data.pdbj.org/pub/pdb/validation_reports/iu/2iup | HTTPS FTP |
-Related structure data
Related structure data | 2hxcC 2iuqC 2iurC 2iuvC 2iva 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.997, 0.073, 0.02), Vector: |
-Components
#1: Protein | Mass: 40016.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ALCALIGENES FAECALIS (bacteria) / Strain: IFO 14479 / References: UniProt: P84888*PLUS, EC: 1.4.99.4 #2: Protein | Mass: 14516.898 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ALCALIGENES FAECALIS (bacteria) / Strain: IFO 14479 / References: UniProt: P84887*PLUS, EC: 1.4.99.4 #3: Water | ChemComp-HOH / | Sequence details | SEQUENCE DATABASE REFERENCES | |
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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: 2.5 Å3/Da / Density % sol: 41 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 91209 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.1 / % possible all: 96 |
-Processing
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Refinement | Method to determine structure: OTHER / Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.179 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.105 / 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: 17.43 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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