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- PDB-5g09: The crystal structure of a S-selective transaminase from Bacillus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5g09 | ||||||
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Title | The crystal structure of a S-selective transaminase from Bacillus megaterium bound with R-alpha-methylbenzylamine | ||||||
![]() | TRANSAMINASE | ||||||
![]() | TRANSFERASE / TRANSAMINASE | ||||||
Function / homology | ![]() Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | van Oosterwijk, N. / Willies, S. / Hekelaar, J. / Terwisscha van Scheltinga, A.C. / Turner, N.J. / Dijkstra, B.W. | ||||||
![]() | ![]() Title: Structural Basis of Substrate Range and Enantioselectivity of Two S-Selective Omega- Transaminases Authors: Van Oosterwijk, N. / Willies, S. / Hekelaar, J. / Terwisscha Van Scheltinga, A.C. / Turner, N.J. / Dijkstra, B.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 390.6 KB | Display | ![]() |
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PDB format | ![]() | 320.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 74.5 KB | Display | |
Data in CIF | ![]() | 106.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g0aC ![]() 5g2pC ![]() 5g2qC ![]() 3gjuS C: citing same article ( S: Starting model for refinement |
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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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 54264.293 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: PYRIDOXAL-5'-PHOSPHATE COVALENTLY BOUND TO R-ALPHA-METHYLBENZYLAMINE Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A1C7D190*PLUS, Transferases; Transferring nitrogenous groups; Transaminases |
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-Non-polymers , 6 types, 934 molecules ![](data/chem/img/6DF.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-6DF / [ #3: Chemical | ChemComp-PGE / #4: Chemical | ChemComp-1PE / | #5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.61 % / Description: NONE |
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Crystal grow | pH: 4.2 Details: 30% PEG300 50 MM NA-PHOSPHATE/CITRATE, PH 4.2 10 MM PYRIDOXAL-5-PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH MAR-225MM / Detector: CCD / Date: Apr 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.5 Å / Num. obs: 149076 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.5 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3GJU Resolution: 1.9→44.46 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.579 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.132 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→44.46 Å
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Refine LS restraints |
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