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- PDB-3pul: Crystal structure of the complex of Dhydrodipicolinate synthase f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pul | ||||||
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Title | Crystal structure of the complex of Dhydrodipicolinate synthase from Acinetobacter baumannii with lysine at 2.3A resolution | ||||||
![]() | Dihydrodipicolinate synthase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jithesh, O. / Yamini, S. / Kaur, N. / Gautam, A. / Tewari, R. / Kushwaha, G.S. / Kaur, P. / Srinivasan, A. / Sharma, S. / Singh, T.P. | ||||||
![]() | ![]() Title: Crystal structure of the complex of Dhydrodipicolinate synthase from Acinetobacter baumannii with lysine at 2.3A resolution Authors: Jithesh, O. / Yamini, S. / Kaur, N. / Gautam, A. / Tewari, R. / Kushwaha, G.S. / Kaur, P. / Srinivasan, A. / Sharma, S. / Singh, T.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.3 KB | Display | ![]() |
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PDB format | ![]() | 98.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3noeS 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: 31279.842 Da / Num. of mol.: 2 / Fragment: DHDPS, residues in UNP 7-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 317 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-LYS / | ![]() #5: Chemical | ChemComp-ACT / | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.25 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion / pH: 5.6 Details: 1.8M ammonium sulphate, 0.1M bis-tris, pH 5.6, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 21, 2010 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→48.7 Å / Num. all: 29562 / Num. obs: 29562 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 39 Å2 / Rsym value: 0.09 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.3→2.34 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.47 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3NOE Resolution: 2.3→47.58 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 6685999.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.822 Å2 / ksol: 0.361261 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→47.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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