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Yorodumi- PDB-6g4b: Crystal structure of the omega transaminase from Pseudomonas jess... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g4b | ||||||
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Title | Crystal structure of the omega transaminase from Pseudomonas jessenii in the apo form, crystallized from succinate | ||||||
Components | Aspartate aminotransferase family protein | ||||||
Keywords | TRANSFERASE / TRANSAMINASE / AMINOTRANSFERASE / PYRIDOXAMINE PHOSPHATE / PLP-DEPENDENT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas sp (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Rozeboom, H.J. / Janssen, D.B. | ||||||
Citation | Journal: Febs J. / Year: 2019 Title: Biochemical properties of a Pseudomonas aminotransferase involved in caprolactam metabolism. Authors: Palacio, C.M. / Rozeboom, H.J. / Lanfranchi, E. / Meng, Q. / Otzen, M. / 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 | 6g4b.cif.gz | 368.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g4b.ent.gz | 299.6 KB | Display | PDB format |
PDBx/mmJSON format | 6g4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g4b_validation.pdf.gz | 445.4 KB | Display | wwPDB validaton report |
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Full document | 6g4b_full_validation.pdf.gz | 446.5 KB | Display | |
Data in XML | 6g4b_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 6g4b_validation.cif.gz | 62.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/6g4b ftp://data.pdbj.org/pub/pdb/validation_reports/g4/6g4b | HTTPS FTP |
-Related structure data
Related structure data | 6g4cC 6g4dC 6g4eC 6g4fC 4grxS 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: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 6 - 455 / Label seq-ID: 6 - 455
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-Components
#1: Protein | Mass: 50727.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Linker PGG and 6-HIS at C-terminus / Source: (gene. exp.) Pseudomonas sp (bacteria) / Gene: CMK94_18730 / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / Variant (production host): C41 / References: UniProt: A0A2D8IND4 #2: Chemical | #3: Chemical | #4: 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: 2.9 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.0 M Sodium succinate, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50.9 Å / Num. obs: 104659 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 16.8 Å2 / Rpim(I) all: 0.038 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4975 / Rpim(I) all: 0.402 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GRX Resolution: 1.8→50.9 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.061 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.086 / 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: 24.737 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→50.9 Å
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Refine LS restraints |
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