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- PDB-8tba: Crystal structure of Helicobacter pylori glutamate racemase bound... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8tba | ||||||
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Title | Crystal structure of Helicobacter pylori glutamate racemase bound to D-glutamate and a crystallographic artifact | ||||||
![]() | Glutamate racemase | ||||||
![]() | ISOMERASE / Enzyme / Epimerase / Gyrase / Artifiact | ||||||
Function / homology | ![]() glutamate racemase / glutamate racemase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Propp, J. / Spies, M.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Helicobacter pylori glutamate racemase bound to D-glutamate and a likely crystallographic artifact Authors: 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 | ![]() | 121.3 KB | Display | ![]() |
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PDB format | ![]() | 91.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 820.3 KB | Display | ![]() |
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Full document | ![]() | 826.9 KB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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
#1: Protein | Mass: 28670.340 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZMX / ( | Mass: 464.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H24N4O3 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 10g/l Glutamate Racemase in crystal buffer (0.2M Ammonium Acetate, 5mM D/L-glutamate, 1mM TCEP, pH 7.4) with 10% DMSO and 2.5mM compound (incubated in fridge for 1 week) combined 2:1 with ...Details: 10g/l Glutamate Racemase in crystal buffer (0.2M Ammonium Acetate, 5mM D/L-glutamate, 1mM TCEP, pH 7.4) with 10% DMSO and 2.5mM compound (incubated in fridge for 1 week) combined 2:1 with INDEX G4 (25% PEG3350, 0.2M LiSO4, 0.1M Tris Base) pH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→79.87 Å / Num. obs: 70675 / % possible obs: 99.8 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.017 / Rrim(I) all: 0.053 / Χ2: 0.89 / Net I/σ(I): 21.7 / Num. measured all: 708160 |
Reflection shell | Resolution: 1.65→1.68 Å / % possible obs: 99.5 % / Redundancy: 10.4 % / Rmerge(I) obs: 1.049 / Num. measured all: 35758 / Num. unique obs: 3437 / CC1/2: 0.871 / Rpim(I) all: 0.335 / Rrim(I) all: 1.103 / Χ2: 0.58 / Net I/σ(I) obs: 2.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→65.58 Å
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Refine LS restraints |
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LS refinement shell |
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