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Yorodumi- PDB-7uj5: Crystal structure of glutamate racemase from Helicobacter pylori ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uj5 | ||||||
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Title | Crystal structure of glutamate racemase from Helicobacter pylori in complex with D-glutamate | ||||||
Components | Glutamate racemase | ||||||
Keywords | ISOMERASE / Racemase / Co-factor independent | ||||||
Function / homology | Function and homology information glutamate racemase / glutamate racemase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Cooling, G.T. / Spies, M.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of glutamate racemase from Helicobacter pylori in complex with D-glutamate Authors: Cooling, G.T. / Spies, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uj5.cif.gz | 395.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uj5.ent.gz | 324.4 KB | Display | PDB format |
PDBx/mmJSON format | 7uj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/7uj5 ftp://data.pdbj.org/pub/pdb/validation_reports/uj/7uj5 | 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 & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28757.562 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: murI, OUM_0701 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K2K6A3, glutamate racemase #2: Chemical | ChemComp-DGL / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.1 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 18-32% PEG4000, 200 mM MgSO4, 100 mM Tris pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0721 Å | ||||||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Dec 7, 2018 | ||||||||||||||||||||||||||||||
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: 1.75→40.06 Å / Num. obs: 111650 / % possible obs: 97.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.78 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.041 / Rrim(I) all: 0.08 / Net I/σ(I): 12.8 / Num. measured all: 409549 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5W1Q Resolution: 1.75→40.06 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.38 / Stereochemistry target values: ML
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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 max: 92.25 Å2 / Biso mean: 28.714 Å2 / Biso min: 10.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→40.06 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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