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Yorodumi- PDB-4uug: The (R)-selective amine transaminase from Aspergillus fumigatus w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uug | ||||||
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Title | The (R)-selective amine transaminase from Aspergillus fumigatus with inhibitor bound | ||||||
Components | AMINE TRANSAMINASE | ||||||
Keywords | TRANSFERASE / GABACULINE | ||||||
Function / homology | Function and homology information Transferases; Transferring nitrogenous groups; Transaminases / carboxylic acid metabolic process / transaminase activity Similarity search - Function | ||||||
Biological species | ASPERGILLUS FUMIGATUS (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Thomsen, M. / Hinrichs, W. | ||||||
Citation | Journal: FEBS J. / Year: 2015 Title: Structural and Biochemical Characterization of the Dual Substrate Recognition of the (R)-Selective Amine Transaminase from Aspergillus Fumigatus Authors: Skalden, L. / Thomsen, M. / Hohne, M. / Bornscheuer, U.T. / Hinrichs, W. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Crystallographic Characterization of the (R)- Selective Amine Transaminase from Aspergillus Fumigatus Authors: Thomsen, M. / Skalden, L. / Palm, G.J. / Hoehne, M. / Bornscheuer, U.T. / Hinrichs, W. | ||||||
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 | 4uug.cif.gz | 316.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uug.ent.gz | 262.2 KB | Display | PDB format |
PDBx/mmJSON format | 4uug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uug_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4uug_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4uug_validation.xml.gz | 36.2 KB | Display | |
Data in CIF | 4uug_validation.cif.gz | 55.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/4uug ftp://data.pdbj.org/pub/pdb/validation_reports/uu/4uug | HTTPS FTP |
-Related structure data
Related structure data | 4chiS S: Starting model for refinement |
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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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99995, 0.00984, 0.00071), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37192.344 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Strain: AF293 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q4WH08, branched-chain-amino-acid transaminase |
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-Non-polymers , 6 types, 805 molecules
#2: Chemical | #3: Chemical | ChemComp-MRD / ( | #4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-MPD / ( | #6: Chemical | ChemComp-NA / | #7: 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: 4 Å3/Da / Density % sol: 69.3 % / Description: NONE |
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Crystal grow | pH: 4.6 / Details: 2.0 M SODIUM FORMATE, 0.1 M SODIUM ACETATE PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2014 / Details: MIRROR |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→47.28 Å / Num. obs: 151504 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CHI Resolution: 1.6→47.25 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.404 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→47.25 Å
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Refine LS restraints |
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