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- PDB-8eb3: Crystal structure of glutamate racemase from Helicobacter pylori ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8eb3 | ||||||
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Title | Crystal structure of glutamate racemase from Helicobacter pylori in complex with a fragment | ||||||
![]() | Glutamate racemase | ||||||
![]() | ISOMERASE / glutamate racemase | ||||||
Function / homology | ![]() glutamate racemase / glutamate racemase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cooling, G.T. / Propp, J. / Spies, M.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of glutamate racemase from Helicobacter pylori in complex with a fragment Authors: Cooling, G.T. / Propp, J. / Spies, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197.5 KB | Display | ![]() |
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PDB format | ![]() | 156.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5w1qS S: Starting model for refinement |
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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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29068.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 155 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/WFI.gif)
![](data/chem/img/DGL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/WFI.gif)
![](data/chem/img/DGL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.87 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.075 mM Tris pH pH 8.47, 150 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Dec 1, 2021 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0721 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→47.99 Å / Num. obs: 26023 / % possible obs: 97.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 34.64 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.037 / Rrim(I) all: 0.07 / Net I/σ(I): 12.4 / Num. measured all: 85935 / Scaling rejects: 3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5W1Q Resolution: 2.2→47.99 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.89 Å2 / Biso mean: 47.5703 Å2 / Biso min: 22.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→47.99 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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