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- PDB-7pji: Crystal structure of Pseudomonas aeruginosa guaB (IMP dehydrogena... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pji | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa guaB (IMP dehydrogenase) bound to ATP and GDP at 1.65A resolution | ||||||
![]() | Inosine-5'-monophosphate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / IMP dehydrogenase / guaB | ||||||
Function / homology | ![]() IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fernandez-Justel, D. / Buey, R.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase. Authors: Fernandez-Justel, D. / Marcos-Alcalde, I. / Abascal, F. / Vidana, N. / Gomez-Puertas, P. / Jimenez, A. / Revuelta, J.L. / Buey, R.M. #1: ![]() Title: Unexpected diversity of ferredoxin-dependent thioredoxin reductases in cyanobacteria. Authors: Buey, R.M. / Fernandez-Justel, D. / Gonzalez-Holgado, G. / Martinez-Julvez, M. / Gonzalez-Lopez, A. / Velazquez-Campoy, A. / Medina, M. / Buchanan, B.B. / Balsera, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 555.1 KB | Display | ![]() |
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PDB format | ![]() | 403.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 39.1 KB | Display | |
Data in CIF | ![]() | 58.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pmzC ![]() 4avfS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 52049.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: guaB, CAZ10_17565, CGU42_10690, CSB93_2499, DT376_00630, DY940_09800, DZ962_03005, E4V10_03770, ECC04_008545, F7O94_09425, H2O03_23015, HW05_11140, IPC1164_08420, IPC116_03070, IPC1295_13460, ...Gene: guaB, CAZ10_17565, CGU42_10690, CSB93_2499, DT376_00630, DY940_09800, DZ962_03005, E4V10_03770, ECC04_008545, F7O94_09425, H2O03_23015, HW05_11140, IPC1164_08420, IPC116_03070, IPC1295_13460, IPC1298_02025, IPC1323_03035, IPC1481_30840, IPC1505_09885, IPC1509_02385, IPC151_02390, IPC36_21115, IPC582_15390, IPC620_11170, IPC737_18950, IPC90_16110, NCTC12924_06429, NCTC13621_00582, NCTC13628_01024, PA52Ts2_5150, PAMH19_1311, RW109_RW109_02018 Production host: ![]() ![]() |
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-Non-polymers , 7 types, 660 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/IMP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/IMP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-ACT / #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.26 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: Condition D11 of the commercial screening Morpheus (Gorrec, 2009): 0.02M Sodium formate; 0.02M Ammonium acetate; 0.02M Sodium citrate tribasic dihydrate; 0.02M Potassium sodium tartrate ...Details: Condition D11 of the commercial screening Morpheus (Gorrec, 2009): 0.02M Sodium formate; 0.02M Ammonium acetate; 0.02M Sodium citrate tribasic dihydrate; 0.02M Potassium sodium tartrate tetrahydrate; 0.02M Sodium oxamate, 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350 in 0.1M of the buffer system Tris (base), bicine, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000008 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50.7 Å / Num. obs: 84861 / % possible obs: 67.8 % / Redundancy: 13.9 % / Biso Wilson estimate: 25.18 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.025 / Rrim(I) all: 0.094 / Net I/σ(I): 13.18 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.76 / Mean I/σ(I) obs: 0.39 / Num. unique obs: 4228 / CC1/2: 0.287 / CC star: 0.668 / Rpim(I) all: 0.489 / Rrim(I) all: 1.827 / % possible all: 7.09 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4AVF Resolution: 1.65→50.7 Å / SU ML: 0.1407 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.44 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 35.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→50.7 Å
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Refine LS restraints |
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LS refinement shell |
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