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- PDB-4nmf: Crystal structure of proline utilization A (PutA) from Geobacter ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nmf | ||||||
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Title | Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine and complexed with menadione bisulfite | ||||||
![]() | Proline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / flavoenzyme / Rossmann fold / aldehyde dehydrogenase / flavin adenine dinucleotide / nicotinamide adenine dinucleotide / proline catabolism / substrate channeling / bifunctional enzyme / mechanism-based inactivation | ||||||
Function / homology | ![]() proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Singh, H. / Tanner, J.J. | ||||||
![]() | ![]() Title: Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site. Authors: Singh, H. / Arentson, B.W. / Becker, D.F. / 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 | ![]() | 772.8 KB | Display | ![]() |
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PDB format | ![]() | 629.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 74.3 KB | Display | |
Data in CIF | ![]() | 108.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nm9C ![]() 4nmaC ![]() 4nmbC ![]() 4nmcSC ![]() 4nmdC ![]() 4nmeC 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, 2 molecules AB
#1: Protein | Mass: 112324.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q746X3, EC: 1.5.99.8, EC: 1.5.1.12, L-glutamate gamma-semialdehyde dehydrogenase |
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-Non-polymers , 5 types, 1020 molecules ![](data/chem/img/P5F.gif)
![](data/chem/img/2L3.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/2LB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/2L3.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/2LB.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-2LB / ( | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25-33% PEG550 MME, 0.05-0.2 M Bis-Tris, pH 6.4-6.5, 0.05 mM calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2013 | |||||||||||||||||||||||||||
Radiation | Monochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.95→47.6 Å / Num. obs: 183582 / % possible obs: 98.5 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.053 / Rrim(I) all: 0.106 / Net I/σ(I): 11.9 / Num. measured all: 691229 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.8 %
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4NMC Resolution: 1.95→47.596 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8654 / SU ML: 0.2 / σ(F): 1.35 / Phase error: 20.63 / 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: 105.1 Å2 / Biso mean: 21.7498 Å2 / Biso min: 6.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→47.596 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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