+Open data
-Basic information
Entry | Database: PDB / ID: 7qyf | ||||||
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Title | Structure of the transaminase PluriZyme variant (TR2E2) | ||||||
Components | Aminotransferase TR2 | ||||||
Keywords | HYDROLASE / transaminase | ||||||
Function / homology | Function and homology information beta-alanine-pyruvate transaminase / beta-alanine-pyruvate transaminase activity / 4-aminobutyrate transaminase activity / gamma-aminobutyric acid metabolic process / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Acidihalobacter (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Roda, S. / Fernandez-Lopez, L. / Benedens, M. / Bollinger, A. / Thies, S. / Schumacher, J. / Coscolin, C. / Kazemi, M. / Santiago, G. / Gertzen, C.G. ...Roda, S. / Fernandez-Lopez, L. / Benedens, M. / Bollinger, A. / Thies, S. / Schumacher, J. / Coscolin, C. / Kazemi, M. / Santiago, G. / Gertzen, C.G. / Gonzalez-Alfonso, J. / Plou, F.J. / Jaeger, K.E. / Smits, S.H. / Ferrer, M. / Guallar, V. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Angew Chem Int Ed Engl / Year: 2022 Title: A Plurizyme with Transaminase and Hydrolase Activity Catalyzes Cascade Reactions. Authors: Roda, S. / Fernandez-Lopez, L. / Benedens, M. / Bollinger, A. / Thies, S. / Schumacher, J. / Coscolin, C. / Kazemi, M. / Santiago, G. / Gertzen, C.G.W. / Gonzalez-Alfonso, J.L. / Plou, F.J. ...Authors: Roda, S. / Fernandez-Lopez, L. / Benedens, M. / Bollinger, A. / Thies, S. / Schumacher, J. / Coscolin, C. / Kazemi, M. / Santiago, G. / Gertzen, C.G.W. / Gonzalez-Alfonso, J.L. / Plou, F.J. / Jaeger, K.E. / Smits, S.H.J. / Ferrer, M. / Guallar, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qyf.cif.gz | 322.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qyf.ent.gz | 263.3 KB | Display | PDB format |
PDBx/mmJSON format | 7qyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qyf_validation.pdf.gz | 469.1 KB | Display | wwPDB validaton report |
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Full document | 7qyf_full_validation.pdf.gz | 512 KB | Display | |
Data in XML | 7qyf_validation.xml.gz | 60.8 KB | Display | |
Data in CIF | 7qyf_validation.cif.gz | 81.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/7qyf ftp://data.pdbj.org/pub/pdb/validation_reports/qy/7qyf | HTTPS FTP |
-Related structure data
Related structure data | 7qx0SC 7qx3C 7qygC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
#1: Protein | Mass: 51658.668 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidihalobacter (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: A0A3G5BC54, beta-alanine-pyruvate transaminase |
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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: 2.81 Å3/Da / Density % sol: 56.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: 200 mM calcium acetate, 100 mM HEPES pH 7.5, 10% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 5, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→39.65 Å / Num. obs: 37886 / % possible obs: 98.45 % / Redundancy: 5.1 % / CC1/2: 0.994 / Net I/σ(I): 7.83 |
Reflection shell | Resolution: 3.3→3.418 Å / Mean I/σ(I) obs: 1.43 / Num. unique obs: 3500 / CC1/2: 0.643 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7QX0 Resolution: 3.3→39.65 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 96.81 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→39.65 Å
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Refine LS restraints |
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