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Yorodumi- PDB-6eoi: Reductive Aminase from Aspergillus terreus in complex with NADPH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eoi | ||||||
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Title | Reductive Aminase from Aspergillus terreus in complex with NADPH and ethyl-5-oxohexanoate | ||||||
Components | Reductive Aminase | ||||||
Keywords | OXIDOREDUCTASE / Amine / Imine / NADPH | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NADP binding Similarity search - Function | ||||||
Biological species | Aspergillus terreus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Sharma, M. / Mangas-Sanchez, J. / Turner, N.J. / Grogan, G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Catalysis / Year: 2018 Title: A Mechanism for Reductive Amination Catalyzed by Fungal Reductive Aminases Authors: Sharma, M. / Mangas-Sanchez, J. / Turner, N.J. / Grogan, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eoi.cif.gz | 123.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eoi.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 6eoi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eoi_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6eoi_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6eoi_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 6eoi_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/6eoi ftp://data.pdbj.org/pub/pdb/validation_reports/eo/6eoi | HTTPS FTP |
-Related structure data
Related structure data | 6eodC 6eohC 5g6sS S: Starting model for refinement 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 domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 6 - 294 / Label seq-ID: 6 - 294
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-Components
#1: Protein | Mass: 30756.084 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus terreus (mold) / Gene: ATEG_08501 / Plasmid: pET-YSBLIC-3C / Production host: Escherichia coli (E. coli) / References: UniProt: Q0CCT3 #2: Chemical | #3: Chemical | #4: Chemical | #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: 2.4 Å3/Da / Density % sol: 49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50 mM Tris-HCl pH 7.5; 0.2 M MgCL2; 25% PEG 3350; 2 mM NADPH; 5 mM ester substrate |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→82.52 Å / Num. obs: 55478 / % possible obs: 99 % / Redundancy: 4.2 % / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.04 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.76→1.79 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3171 / CC1/2: 0.94 / Rpim(I) all: 0.47 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5G6S Resolution: 1.76→82.52 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.061 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.119 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.563 Å2
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Refinement step | Cycle: 1 / Resolution: 1.76→82.52 Å
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Refine LS restraints |
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