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Open data
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Basic information
Entry | Database: PDB / ID: 4a8j | ||||||
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Title | Crystal Structure of the Elongator subcomplex Elp456 | ||||||
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![]() | TRANSCRIPTION | ||||||
Function / homology | ![]() elongator holoenzyme complex / protein urmylation / tRNA wobble uridine modification / tRNA modification / transcription elongation factor complex / regulation of translation / tRNA binding / regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding ...elongator holoenzyme complex / protein urmylation / tRNA wobble uridine modification / tRNA modification / transcription elongation factor complex / regulation of translation / tRNA binding / regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Glatt, S. / Mueller, C.W. | ||||||
![]() | ![]() Title: The Elongator Subcomplex Elp456 is a Hexameric Reca-Like ATPase. Authors: Glatt, S. / Letoquart, J. / Faux, C. / Taylor, N.M.I. / Seraphin, B. / Muller, C.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 338.9 KB | Display | ![]() |
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PDB format | ![]() | 270.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.3 KB | Display | ![]() |
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Full document | ![]() | 497.7 KB | Display | |
Data in XML | ![]() | 63.3 KB | Display | |
Data in CIF | ![]() | 90.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 41329.605 Da / Num. of mol.: 2 / Fragment: RESIDUES 66-426 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S288C / Plasmid: PET24D / Production host: ![]() ![]() #2: Protein | Mass: 31045.268 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S288C / Plasmid: PET24D / Production host: ![]() ![]() #3: Protein | Mass: 31797.154 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S288C / Plasmid: PET24D / Production host: ![]() ![]() #4: Water | ChemComp-HOH / | Sequence details | 6XHIS TAG AT THE N-TERMINUS (MHHHHHHH) | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.4 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 200 MM MGCL2, 100 MM TRISHCL PH 7.5, AND 25% PEG 2K MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9782 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.2 Å / Num. obs: 112115 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 30.48 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.56 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.1→46.2 Å / SU ML: 0.49 / σ(F): 2 / Phase error: 29.75 / Stereochemistry target values: ML Details: TWO REGIONS IN ELP4 RESIDUES 137-144 AND 169-233, TWO SHORT LOOPS IN ELP5 AND ITS C--TERMINUS RESIDUES 93-98, 144-148 AND 233-270 AND TWO SHORT LOOPS AND THE N-TERMINAL 6XHIS-TAG OF ELP6 ...Details: TWO REGIONS IN ELP4 RESIDUES 137-144 AND 169-233, TWO SHORT LOOPS IN ELP5 AND ITS C--TERMINUS RESIDUES 93-98, 144-148 AND 233-270 AND TWO SHORT LOOPS AND THE N-TERMINAL 6XHIS-TAG OF ELP6 RESIDUES 64-66 AND 227-231 ARE DISORDERD.
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.7 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→46.2 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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