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- PDB-5m42: Structure of Thermus thermophilus L-proline dehydrogenase lacking... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5m42 | |||||||||
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Title | Structure of Thermus thermophilus L-proline dehydrogenase lacking alpha helices A, B and C | |||||||||
![]() | Proline dehydrogenase![]() | |||||||||
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Function / homology | ![]() proline catabolic process / ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Martinez-Julvez, M. / Huijbers, M.M.E. / van Berkel, W.J.H. / Medina, M. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Proline dehydrogenase from Thermus thermophilus does not discriminate between FAD and FMN as cofactor. Authors: Huijbers, M.M. / Martinez-Julvez, M. / Westphal, A.H. / Delgado-Arciniega, E. / Medina, M. / van Berkel, W.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.7 KB | Display | ![]() |
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PDB format | ![]() | 47.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2g37S 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
#1: Protein | ![]() Mass: 32426.514 Da / Num. of mol.: 1 / Mutation: Delection of alpha helices A,B and C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FMN / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.7 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 20 % v/v 2-propanol, 0.2 M calcium chloride dihydrate and 0.1 M sodium acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→65.96 Å / Num. obs: 18892 / % possible obs: 100 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 8.7 % / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2G37 Resolution: 2.2→60.01 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.356 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.171
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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: 37.672 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→60.01 Å
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Refine LS restraints |
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