+Open data
-Basic information
Entry | Database: PDB / ID: 5cqs | ||||||
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Title | Dimerization of Elp1 is essential for Elongator complex assembly | ||||||
Components | Elongator complex protein 1 | ||||||
Keywords | PROTEIN BINDING / Familial Dysautonomia / Elongator Complex / Elp1 subunit / dimerization | ||||||
Function / homology | Function and homology information elongator holoenzyme complex / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / : / protein transport / regulation of translation / tRNA binding / regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding ...elongator holoenzyme complex / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / : / protein transport / regulation of translation / tRNA binding / regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Lin, Z. / Xu, H. / Li, F. / Diao, W. / Long, J. / Shen, Y. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Dimerization of elongator protein 1 is essential for Elongator complex assembly. Authors: Xu, H. / Lin, Z. / Li, F. / Diao, W. / Dong, C. / Zhou, H. / Xie, X. / Wang, Z. / Shen, Y. / Long, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cqs.cif.gz | 500.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cqs.ent.gz | 429.9 KB | Display | PDB format |
PDBx/mmJSON format | 5cqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/5cqs ftp://data.pdbj.org/pub/pdb/validation_reports/cq/5cqs | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 50226.488 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 919-1349 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: IKI3, ELP1, TOT1, YLR384C, L3502.7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06706 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100mM HEPES, pH 7.5, 300 mM MgCl2, 38.0% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 75588 / % possible obs: 99.9 % / Redundancy: 3.8 % / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→45.788 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.46 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→45.788 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 61.5768 Å / Origin y: 41.1076 Å / Origin z: 36.9801 Å
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Refinement TLS group | Selection details: all |