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- PDB-4rkc: Psychrophilic aromatic amino acids aminotransferase from Psychrob... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rkc | ||||||
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Title | Psychrophilic aromatic amino acids aminotransferase from Psychrobacter sp. B6 | ||||||
![]() | Aromatic amino acid aminotransferase | ||||||
![]() | TRANSFERASE / AMINOTRANSFERASE / AROMATIC SUBSTRATES / PLP Dependent ENZYME / PLP | ||||||
Function / homology | ![]() Transferases; Transferring nitrogenous groups; Transaminases / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / pyridoxal phosphate binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bujacz, A. / Rutkiewicz-Krotewicz, M. / Bujacz, G. / Nowakowska-Sapota, K. / Turkiewicz, M. | ||||||
![]() | ![]() Title: Crystal structure and enzymatic properties of a broad substrate-specificity psychrophilic aminotransferase from the Antarctic soil bacterium Psychrobacter sp. B6. Authors: Bujacz, A. / Rutkiewicz-Krotewicz, M. / Nowakowska-Sapota, K. / Turkiewicz, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 328.9 KB | Display | ![]() |
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PDB format | ![]() | 268.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.6 KB | Display | ![]() |
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Full document | ![]() | 489.2 KB | Display | |
Data in XML | ![]() | 40 KB | Display | |
Data in CIF | ![]() | 60 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rkdC ![]() 3fslS ![]() 3qn6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44199.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: C7E5X4, aromatic-amino-acid transaminase #2: Chemical | #3: Chemical | ChemComp-NO3 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M Mg(NO3)2, 20% PEG3350, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 9, 2011 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.802 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→50 Å / Num. obs: 39647 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 16.67 |
Reflection shell | Resolution: 2.19→2.27 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 3.72 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3FSL and 3QN6 Resolution: 2.19→43 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.554 / SU ML: 0.119 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.277 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.137 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.246 Å / 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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