[English] 日本語
![](img/lk-miru.gif)
- PDB-6vz9: Structure of proline utilization A with the FAD covalently modifi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6vz9 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of proline utilization A with the FAD covalently modified by L-thiazolidine-2-carboxylate | |||||||||
![]() | Bifunctional protein PutA | |||||||||
![]() | OXIDOREDUCTASE / FLAVOENZYME / ROSSMANN FOLD / PROLINE CATABOLISM / SUBSTRATE CHANNELING / BIFUNCTIONAL ENZYME | |||||||||
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 / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding / DNA binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Campbell, A.C. / Tanner, J.J. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Covalent Modification of the Flavin in Proline Dehydrogenase by Thiazolidine-2-Carboxylate. Authors: Campbell, A.C. / Becker, D.F. / Gates, K.S. / Tanner, J.J. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 958.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 778.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 626 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 648.8 KB | Display | |
Data in XML | ![]() | 3.7 KB | Display | |
Data in CIF | ![]() | 39.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ufpC ![]() 5kf6S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 131961.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: SM11 / Gene: putA, SM11_chr0102 / Production host: ![]() ![]() References: UniProt: F7X6I3, proline dehydrogenase, L-glutamate gamma-semialdehyde dehydrogenase |
---|
-Non-polymers , 8 types, 2384 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/T2C.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/T2C.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-PGE / | #9: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.06 % |
---|---|
Crystal grow | Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% PEG-3350, 0.2M AMMONIUM SULFATE, REMARK 280 0.1M MGCL2, 0.1M HEPES, 0.1M NA FORMATE, 10MM NAD+, 50MM thiazolidine-2-carboxylate, PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Feb 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→48.44 Å / Num. obs: 708036 / % possible obs: 99.1 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.048 / Rrim(I) all: 0.091 / Net I/σ(I): 10.9 / Num. measured all: 1321174 / Scaling rejects: 302 |
Reflection shell | Resolution: 1.52→1.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.377 / Num. measured all: 53582 / Num. unique obs: 17048 / CC1/2: 0.354 / Rpim(I) all: 0.916 / Rrim(I) all: 1.663 / Net I/σ(I) obs: 0.7 / % possible all: 91.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5KF6 Resolution: 1.52→48.44 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.97 / Phase error: 22.26
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.19 Å2 / Biso mean: 24.44 Å2 / Biso min: 8.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.52→48.44 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|