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- PDB-7sqn: Structure of the E. coli PutA proline dehydrogenase domain (resid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7sqn | ||||||
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Title | Structure of the E. coli PutA proline dehydrogenase domain (residues 86-630) complexed with (2S)-oxetane-2-carboxylic acid | ||||||
![]() | Bifunctional protein PutA | ||||||
![]() | OXIDOREDUCTASE / BETA/ALPHA BARREL / FLAVOENZYME / PROLINE CATABOLISM | ||||||
Function / homology | (2S)-oxetane-2-carboxylic acid / FLAVIN-ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tanner, J.J. / Bogner, A.N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-affinity relationships of reversible proline analog inhibitors targeting proline dehydrogenase. Authors: Bogner, A.N. / 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 | ![]() | 210 KB | Display | ![]() |
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PDB format | ![]() | 163.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mwtC ![]() 7mwuSC ![]() 7mwvC 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 61451.102 Da / Num. of mol.: 1 / Fragment: residues 86-630 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A383H020, proline dehydrogenase, L-glutamate gamma-semialdehyde dehydrogenase |
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-Non-polymers , 5 types, 62 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/A8G.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/A8G.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / |
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#3: Chemical | ChemComp-PGE / |
#4: Chemical | ChemComp-1PE / |
#5: Chemical | ChemComp-A8G / ( |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.24 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 100 mM sodium citrate pH 5.6, 5.75, 5.9 or 6.0 and 18-28% PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→64.72 Å / Num. obs: 35985 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 55.05 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.053 / Rrim(I) all: 0.126 / Net I/σ(I): 6.3 / Num. measured all: 191098 / Scaling rejects: 86 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7MWU Resolution: 2.25→64.72 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 153.66 Å2 / Biso mean: 69.6152 Å2 / Biso min: 37.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→64.72 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Origin x: 4.9795 Å / Origin y: 49.4039 Å / Origin z: 49.3375 Å
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Refinement TLS group | Selection details: chain A and peptide |