+Open data
-Basic information
Entry | Database: PDB / ID: 6xu3 | ||||||
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Title | (R)-selective amine transaminase from Shinella sp. | ||||||
Components | Class IV aminotransferase | ||||||
Keywords | TRANSFERASE / fold IV PLP-dependent enzyme / amine transaminase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shinella sp. JR1-6 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Telzerow, A. / Hakansson, M. / Steiner, K. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Chembiochem / Year: 2021 Title: Expanding the Toolbox of R-Selective Amine Transaminases by Identification and Characterization of New Members. Authors: Telzerow, A. / Paris, J. / Hakansson, M. / Gonzalez-Sabin, J. / Rios-Lombardia, N. / Groger, H. / Moris, F. / Schurmann, M. / Schwab, H. / Steiner, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xu3.cif.gz | 535.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xu3.ent.gz | 414.6 KB | Display | PDB format |
PDBx/mmJSON format | 6xu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xu3_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6xu3_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6xu3_validation.xml.gz | 53.7 KB | Display | |
Data in CIF | 6xu3_validation.cif.gz | 76.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/6xu3 ftp://data.pdbj.org/pub/pdb/validation_reports/xu/6xu3 | HTTPS FTP |
-Related structure data
Related structure data | 6snlC 4ce5S 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 36734.863 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shinella sp. JR1-6 (bacteria) / Gene: EXZ48_21850 / Plasmid: pEHISTEV / Cell line (production host): BL21-Gold(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Q8MG35 |
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-Non-polymers , 8 types, 633 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-NO3 / #6: Chemical | ChemComp-PEG / | #7: Chemical | #8: Chemical | ChemComp-GAB / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.34 Å3/Da / Density % sol: 47.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: sodium nitrate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.099→46.04 Å / Num. obs: 81122 / % possible obs: 99.48 % / Redundancy: 6.8 % / Biso Wilson estimate: 33.38 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1346 / Rpim(I) all: 0.05517 / Rrim(I) all: 0.1457 / Net I/σ(I): 10.94 |
Reflection shell | Resolution: 2.099→2.174 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.291 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 7727 / CC1/2: 0.581 / CC star: 0.857 / Rpim(I) all: 0.5618 / % possible all: 96.23 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CE5 Resolution: 2.1→46.04 Å / SU ML: 0.2739 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.1561
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.04 Å
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Refine LS restraints |
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LS refinement shell |
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