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- PDB-4dgt: Crystal structure of PLP-bound putative aminotransferase from Clo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dgt | ||||||
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Title | Crystal structure of PLP-bound putative aminotransferase from Clostridium difficile 630 crystallized with magnesium formate | ||||||
![]() | Putative pyridoxal phosphate-dependent transferase | ||||||
![]() | TRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / internal aldimine with pyridoxalphosphate | ||||||
Function / homology | ![]() cysteine-S-conjugate beta-lyase / biosynthetic process / pyridoxal phosphate binding / transferase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shabalin, I.G. / Onopriyenko, O. / Kudritska, M. / Chruszcz, M. / Grimshaw, S. / Porebski, P.J. / Cooper, D.R. / Savchenko, A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: Crystal structures of putative aminotransferase from Clostridium difficile 630 Authors: Shabalin, I.G. / Onopriyenko, O. / Kudritska, M. / Grimshaw, S. / Chruszcz, M. / Porebski, P.J. / Cooper, D.R. / Savchenko, A. / Anderson, W.F. / Minor, 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 | ![]() | 334.9 KB | Display | ![]() |
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PDB format | ![]() | 270.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.9 KB | Display | ![]() |
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Full document | ![]() | 468.3 KB | Display | |
Data in XML | ![]() | 38.8 KB | Display | |
Data in CIF | ![]() | 60.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dq6C ![]() 3t32S S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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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: 45086.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25% PEG 3350, 2M Mg Formate, pH 7.0, vapor diffusion, hanging drop, temperature 20K, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 6, 2011 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. all: 99598 / Num. obs: 99100 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4608 / Rsym value: 0.407 / % possible all: 94.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: SwissModel generated model based on PDB ENTRY 3T32 structure Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.755 / SU ML: 0.052 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.078 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.62 Å2 / Biso mean: 17.2009 Å2 / Biso min: 7.41 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 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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