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- PDB-5udr: LarE, a sulfur transferase involved in synthesis of the cofactor ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5udr | ||||||
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Title | LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in complex with nicotinamide mononucleotid NMN | ||||||
![]() | ATP-utilizing enzyme of the PP-loopsuperfamily | ||||||
![]() | TRANSFERASE / Lar / sulfur transferase / LarE / AMPylation / hexamer / trimer / PP-loop / ATP pyrophophatase domain / lactate / lactate racemization / lactate racemase | ||||||
Function / homology | ![]() pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase / NAD+ synthase (glutamine-hydrolyzing) activity / sulfurtransferase activity / lyase activity / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Fellner, M. / Desguin, B. / Hausinger, R.P. / Hu, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE. Authors: Fellner, M. / Desguin, B. / Hausinger, R.P. / Hu, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 292.8 KB | Display | ![]() |
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PDB format | ![]() | 235 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 54.6 KB | Display | |
Data in CIF | ![]() | 71.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5udqC ![]() 5udsC ![]() 5udtC ![]() 5uduC ![]() 5udvC ![]() 5udwC ![]() 5udxC ![]() 5unmC C: citing same article ( |
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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
#1: Protein | Mass: 31718.766 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: A8P51_04975, IV39_GL000116, Nizo1839_0768, Nizo2891_3302, SRCM101060_01452 Plasmid: pGIR076 / Production host: ![]() ![]() #2: Chemical | ChemComp-NMN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.68 % / Mosaicity: 0.14 ° |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 5 ul 23 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) was mixed with 5 ul of reservoir solution. Hanging drop reservoir contained 100 ul of 30.0% v/v pentaerythritol ethoxylate (15/4 ...Details: 5 ul 23 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) was mixed with 5 ul of reservoir solution. Hanging drop reservoir contained 100 ul of 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 150 mM ammonium sulfate. Crystals grew to full size within 4 days and remained in the drop for 4 months without notable changes. A single crystal was then transfered to a 10 ul drop containing ~100 mM beta-nicotinamide mononucleotide, 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH) and 50 mM BIS-TRIS pH 6.5. The drop was incubated for 11 days over a hanging drop reservoir containing 100 ul of 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 100 mM ammonium sulfate before being directly frozen. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 25, 2016 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.62→48.42 Å / Num. obs: 59143 / % possible obs: 99.9 % / Redundancy: 12.2 % / Biso Wilson estimate: 58.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Net I/σ(I): 21.3 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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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: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.94 Å2 / Biso mean: 61.9946 Å2 / Biso min: 28.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.62→48.42 Å
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Refine LS restraints |
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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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