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Yorodumi- PDB-5w16: Crystal structure of glutamate racemase from Thermus thermophilus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w16 | ||||||
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Title | Crystal structure of glutamate racemase from Thermus thermophilus in complex with D-glutamate | ||||||
Components | Glutamate racemase | ||||||
Keywords | ISOMERASE / Thermophile / Racemase / Cofactor-independent / D-glutamate | ||||||
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 | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.909 Å | ||||||
Authors | Cooling, G.T. / Vance, N.R. / Spies, M.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of glutamate racemase from Thermus Thermophilus in complex with D-glutamate Authors: Cooling, G.T. / Vance, N.R. / 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 | 5w16.cif.gz | 391.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w16.ent.gz | 318.2 KB | Display | PDB format |
PDBx/mmJSON format | 5w16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/5w16 ftp://data.pdbj.org/pub/pdb/validation_reports/w1/5w16 | HTTPS FTP |
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-Related structure data
Related structure data | 5hj7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29958.516 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: murI, TTHA1643 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q5SHT7, UniProt: A0A1J1ER74*PLUS, glutamate racemase #2: Chemical | ChemComp-DGL / #3: Chemical | ChemComp-NO3 / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
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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: 2.95 Å3/Da / Density % sol: 58.32 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 2.5 M ammonium nitrate / PH range: 8.0-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: May 13, 2017 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→62.41 Å / Num. obs: 112287 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.045 / Rrim(I) all: 0.087 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 16206 / CC1/2: 0.741 / Rpim(I) all: 0.891 / Rrim(I) all: 1.664 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5HJ7 Resolution: 1.909→58.929 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.909→58.929 Å
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Refine LS restraints |
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LS refinement shell |
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