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- PDB-5cqs: Dimerization of Elp1 is essential for Elongator complex assembly -

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Basic information

Entry
Database: PDB / ID: 5cqs
TitleDimerization of Elp1 is essential for Elongator complex assembly
ComponentsElongator complex protein 1
KeywordsPROTEIN 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
Elongator complex protein 1 / IKI3 family
Similarity search - Domain/homology
Elongator complex protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsLin, Z. / Xu, H. / Li, F. / Diao, W. / Long, J. / Shen, Y.
CitationJournal: 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
DepositionJul 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Experimental preparation
Revision 1.3Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongator complex protein 1
B: Elongator complex protein 1
C: Elongator complex protein 1
D: Elongator complex protein 1


Theoretical massNumber of molelcules
Total (without water)200,9064
Polymers200,9064
Non-polymers00
Water37821
1
A: Elongator complex protein 1
D: Elongator complex protein 1


Theoretical massNumber of molelcules
Total (without water)100,4532
Polymers100,4532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-9 kcal/mol
Surface area32490 Å2
MethodPISA
2
B: Elongator complex protein 1
C: Elongator complex protein 1


Theoretical massNumber of molelcules
Total (without water)100,4532
Polymers100,4532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-6 kcal/mol
Surface area32710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.754, 157.744, 139.264
Angle α, β, γ (deg.)90.00, 93.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Elongator complex protein 1 / Gamma-toxin target 1 / Protein IKI3


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 / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100mM HEPES, pH 7.5, 300 mM MgCl2, 38.0% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 75588 / % possible obs: 99.9 % / Redundancy: 3.8 % / Net I/σ(I): 21.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.256 7379 9.89 %
Rwork0.2341 --
obs0.2363 74618 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→45.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9978 0 0 21 9999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810139
X-RAY DIFFRACTIONf_angle_d1.11913733
X-RAY DIFFRACTIONf_dihedral_angle_d17.5253685
X-RAY DIFFRACTIONf_chiral_restr0.081555
X-RAY DIFFRACTIONf_plane_restr0.0041794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6955-2.72610.36012160.33941986X-RAY DIFFRACTION87
2.7261-2.75820.35362270.3412219X-RAY DIFFRACTION97
2.7582-2.79180.3692540.34362172X-RAY DIFFRACTION98
2.7918-2.82720.37862590.32812271X-RAY DIFFRACTION98
2.8272-2.86440.33462310.30422198X-RAY DIFFRACTION98
2.8644-2.90360.33212430.29142289X-RAY DIFFRACTION99
2.9036-2.94510.2762530.29492166X-RAY DIFFRACTION98
2.9451-2.9890.31332620.29412256X-RAY DIFFRACTION99
2.989-3.03570.3042510.27562232X-RAY DIFFRACTION99
3.0357-3.08550.31292570.28672254X-RAY DIFFRACTION99
3.0855-3.13870.34172460.28052214X-RAY DIFFRACTION99
3.1387-3.19570.29172640.27822254X-RAY DIFFRACTION99
3.1957-3.25720.31462380.27222234X-RAY DIFFRACTION98
3.2572-3.32360.2692400.25822230X-RAY DIFFRACTION99
3.3236-3.39590.27622490.24992264X-RAY DIFFRACTION99
3.3959-3.47490.26712320.2332251X-RAY DIFFRACTION99
3.4749-3.56170.27452370.2382277X-RAY DIFFRACTION99
3.5617-3.6580.2642350.22952282X-RAY DIFFRACTION99
3.658-3.76560.23382390.20342298X-RAY DIFFRACTION99
3.7656-3.88710.23422500.20242241X-RAY DIFFRACTION99
3.8871-4.02590.22452640.20352223X-RAY DIFFRACTION99
4.0259-4.1870.22082320.19962287X-RAY DIFFRACTION99
4.187-4.37740.22782300.20132313X-RAY DIFFRACTION100
4.3774-4.6080.20122580.19762268X-RAY DIFFRACTION99
4.608-4.89640.25352470.2132225X-RAY DIFFRACTION99
4.8964-5.27390.23532290.23232290X-RAY DIFFRACTION99
5.2739-5.80370.29412870.25542239X-RAY DIFFRACTION99
5.8037-6.64140.30022470.25962256X-RAY DIFFRACTION99
6.6414-8.35910.19972590.20952281X-RAY DIFFRACTION99
8.3591-45.79460.222430.21082269X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 61.5768 Å / Origin y: 41.1076 Å / Origin z: 36.9801 Å
111213212223313233
T0.6704 Å2-0.2532 Å20.0059 Å2-0.533 Å2-0.0103 Å2--0.3665 Å2
L0.2248 °20.2399 °20.02 °2-0.3455 °2-0.0056 °2--0.4054 °2
S-0.0995 Å °0.0587 Å °-0.0522 Å °-0.2057 Å °0.0564 Å °-0.0342 Å °0.0859 Å °-0.0399 Å °0.037 Å °
Refinement TLS groupSelection details: all

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