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Yorodumi- PDB-6tb0: Crystal structure of thermostable omega transaminase 4-fold mutan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tb0 | ||||||
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Title | Crystal structure of thermostable omega transaminase 4-fold mutant from Pseudomonas jessenii | ||||||
Components | Aspartate aminotransferase family protein | ||||||
Keywords | TRANSFERASE / transaminase / aminotransferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.95 Å | ||||||
Authors | Capra, N. / Rozeboom, H.J. / Thunnissen, A.M.W.H. / Janssen, D.B. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: Acs Catalysis / Year: 2020 Title: Robust omega-Transaminases by Computational Stabilization of the Subunit Interface. Authors: Meng, Q. / Capra, N. / Palacio, C.M. / Lanfranchi, E. / Otzen, M. / van Schie, L.Z. / Rozeboom, H.J. / Thunnissen, A.W.H. / Wijma, H.J. / Janssen, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tb0.cif.gz | 367.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tb0.ent.gz | 298 KB | Display | PDB format |
PDBx/mmJSON format | 6tb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/6tb0 ftp://data.pdbj.org/pub/pdb/validation_reports/tb/6tb0 | HTTPS FTP |
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-Related structure data
Related structure data | 6tb1C 6g4bS 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: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 6 - 455 / Label seq-ID: 1 - 450
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-Components
#1: Protein | Mass: 49326.301 Da / Num. of mol.: 2 / Mutation: P9A, E38Q, S87D, I154V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: CMK94_18730, DIU04_17820 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2D8IND4 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SIN / | #5: Water | ChemComp-HOH / | 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: 2.88 Å3/Da / Density % sol: 57.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: Succinic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å | ||||||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 31, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.95→49.08 Å / Num. obs: 82063 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Net I/σ(I): 16.7 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6G4B Resolution: 1.95→49.08 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 5.278 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.106 Details: U VALUES : WITH TLS ADDED 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 max: 257.14 Å2 / Biso mean: 25.461 Å2 / Biso min: 6.88 Å2
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Refinement step | Cycle: final / Resolution: 1.95→49.08 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 14690 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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