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Open data
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Basic information
Entry | Database: PDB / ID: 5eez | ||||||
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Title | RADIATION DAMAGE TO THE TRAP-RNA COMPLEX: DOSE (DWD) 14.2 MGy | ||||||
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![]() | RNA BINDING PROTEIN / protein-RNA complex / radiation damage | ||||||
Function / homology | ![]() DNA-templated transcription termination / regulation of DNA-templated transcription / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bury, C.S. / McGeehan, J.E. / Garman, E.F. / Shevtsov, M.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: RNA protects a nucleoprotein complex against radiation damage. Authors: Bury, C.S. / McGeehan, J.E. / Antson, A.A. / Carmichael, I. / Gerstel, M. / Shevtsov, M.B. / Garman, E.F. #1: ![]() Title: Specificity of TRAP-RNA interactions: crystal structures of two complexes with different RNA sequences. Authors: Hopcroft, N.H. / Wendt, A.L. / Gollnick, P. / Antson, A.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 | ![]() | 348.4 KB | Display | ![]() |
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PDB format | ![]() | 280.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 623.9 KB | Display | ![]() |
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Full document | ![]() | 658.8 KB | Display | |
Data in XML | ![]() | 62.8 KB | Display | |
Data in CIF | ![]() | 93.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5eeuSC ![]() 5eevC ![]() 5eewC ![]() 5eexC ![]() 5eeyC ![]() 5ef0C ![]() 5ef1C ![]() 5ef2C ![]() 5ef3C S: Starting model for refinement 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8257.377 Da / Num. of mol.: 22 / Fragment: TRP RNA-BINDING ATTENUATION PROTEIN (TRAP) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: mtrB / Plasmid: PTZSTMTRB / Production host: ![]() ![]() #2: RNA chain | ( | Mass: 17906.479 Da / Num. of mol.: 1 / Fragment: (GAGUU)10GAG 53-NUCLEOTIDE RNA / Source method: obtained synthetically / Details: SYNTHETIC RNA. IN-VITRO TRANSCRIPTION / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-TRP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.11 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: Potassium phosphate,L-tryptophan,potassium glutamate,triethanolamine,MgCl2,monomethyl ether PEG 2000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2010 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.98→62.66 Å / Num. obs: 130738 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 32.68 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.068 / Net I/σ(I): 8.1 / Num. measured all: 476499 / Scaling rejects: 15 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5eeu Resolution: 1.98→58.638 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.49 / 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: 112.61 Å2 / Biso mean: 40.3147 Å2 / Biso min: 21.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.98→58.638 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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