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Open data
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Basic information
Entry | Database: PDB / ID: 1hru | ||||||
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Title | THE STRUCTURE OF THE YRDC GENE PRODUCT FROM E.COLI | ||||||
![]() | YRDC GENE PRODUCT | ||||||
![]() | UNKNOWN FUNCTION / protein folding / structural genomics / RNA / Sua5 / YrdC / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | ![]() L-threonylcarbamoyladenylate synthase / L-threonylcarbamoyladenylate synthase / tRNA threonylcarbamoyladenosine modification / regulation of translational fidelity / nucleotidyltransferase activity / rRNA processing / double-stranded RNA binding / tRNA binding / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Teplova, M. / Tereshko, V. / Sanishvili, R. / Joachimiak, A. / Bushueva, T. / Anderson, W.F. / Egli, M. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding. Authors: Teplova, M. / Tereshko, V. / Sanishvili, R. / Joachimiak, A. / Bushueva, T. / Anderson, W.F. / Egli, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.1 KB | Display | ![]() |
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PDB format | ![]() | 71 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.1 KB | Display | ![]() |
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Full document | ![]() | 455.7 KB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 30.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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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: 20695.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.31 % | ||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: sodium potassium phosphate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K | ||||||||||||||||||||
Crystal grow | *PLUS Details: used seeding | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Apr 26, 1999 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.96→30 Å / Num. all: 62780 / Num. obs: 62780 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.68 % / Biso Wilson estimate: 5.6 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.6 | ||||||||||||
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 3.65 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.6 / Num. unique all: 23642 / % possible all: 99.8 | ||||||||||||
Reflection | *PLUS Num. measured all: 230966 | ||||||||||||
Reflection shell | *PLUS % possible obs: 99.8 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.84 Å2 / ksol: 0.354 e/Å3 | |||||||||||||||||||||
Displacement parameters | Biso mean: 25.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→22.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10.2 % | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.8 Å2 | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.236 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.217 |