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- PDB-1tj2: Crystal structure of E. coli PutA proline dehydrogenase domain (r... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1tj2 | ||||||
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Title | Crystal structure of E. coli PutA proline dehydrogenase domain (residues 86-669) complexed with acetate | ||||||
![]() | Bifunctional putA protein | ||||||
![]() | OXIDOREDUCTASE / beta/alpha barrel / flavoenzyme / FAD / proline catabolism | ||||||
Function / homology | ![]() proline dehydrogenase / proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / proline biosynthetic process / DNA-binding transcription repressor activity / cis-regulatory region sequence-specific DNA binding / cytoplasmic side of plasma membrane / flavin adenine dinucleotide binding ...proline dehydrogenase / proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / proline biosynthetic process / DNA-binding transcription repressor activity / cis-regulatory region sequence-specific DNA binding / cytoplasmic side of plasma membrane / flavin adenine dinucleotide binding / response to oxidative stress / sequence-specific DNA binding / negative regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tanner, J.J. / Zhang, M. / White, T.A. / Schuermann, J.P. / Baban, B.A. / Becker, D.F. | ||||||
![]() | ![]() Title: Structures of the Escherichia coli PutA proline dehydrogenase domain in complex with competitive inhibitors Authors: Zhang, M. / White, T.A. / Schuermann, J.P. / Baban, B.A. / Becker, D.F. / Tanner, J.J. #1: ![]() Title: Detection of L-lactate in polyethylene glycol solutions confirms the identity of the active-site ligand in a proline dehydrogenase structure Authors: Zhang, M. / Tanner, J.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 | ![]() | 110.7 KB | Display | ![]() |
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PDB format | ![]() | 81 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1tiwC ![]() 1tj0C ![]() 1tj1C ![]() 1k87 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 64665.871 Da / Num. of mol.: 1 Fragment: E. coli PutA proline dehydrogenase domain (residues 86-669) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-FAD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: 13-15 % PEG 3350, 60-190 mM citrate buffer, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Nov 15, 2003 / Details: APS 19ID |
Radiation | Monochromator: APS 19ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→99 Å / Num. all: 46790 / Num. obs: 45470 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4232 / Rsym value: 0.405 / % possible all: 91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1k87 ![]() 1k87 Resolution: 2.05→22.7 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.693 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.158 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.081 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→22.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 6.827 Å / Origin y: 45.312 Å / Origin z: 52.439 Å
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Refinement TLS group |
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