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- PDB-4ejs: Structure of yeast elongator subcomplex Elp456 -

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Basic information

Entry
Database: PDB / ID: 4ejs
TitleStructure of yeast elongator subcomplex Elp456
Components
  • Elongator complex protein 4
  • Elongator complex protein 5
  • Elongator complex protein 6
KeywordsTRANSCRIPTION / Elongator subcomplex Elp456 / RecA-ATPase-like domain fold
Function / homology
Function and homology information


elongator holoenzyme complex / protein urmylation / tRNA wobble uridine modification / tRNA modification / transcription elongation factor complex / regulation of translation / regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus ...elongator holoenzyme complex / protein urmylation / tRNA wobble uridine modification / tRNA modification / transcription elongation factor complex / regulation of translation / regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Elongator complex protein 4 / Elongator complex protein 6 / Elongator complex protein 5 / PAXNEB protein / Elongator subunit Iki1 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Elongator complex protein 5 / Elongator complex protein 4 / Elongator complex protein 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.606 Å
AuthorsLin, Z. / Zhao, W. / Long, J. / Shen, Y.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal structure of elongator subcomplex Elp4-6
Authors: Lin, Z. / Zhao, W. / Diao, W. / Xie, X. / Wang, Z. / Zhang, J. / Shen, Y. / Long, J.
History
DepositionApr 7, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongator complex protein 4
B: Elongator complex protein 5
C: Elongator complex protein 6


Theoretical massNumber of molelcules
Total (without water)100,7543
Polymers100,7543
Non-polymers00
Water34219
1
A: Elongator complex protein 4
B: Elongator complex protein 5
C: Elongator complex protein 6

A: Elongator complex protein 4
B: Elongator complex protein 5
C: Elongator complex protein 6


Theoretical massNumber of molelcules
Total (without water)201,5096
Polymers201,5096
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area12160 Å2
ΔGint-67 kcal/mol
Surface area55470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.513, 186.513, 186.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Elongator complex protein 4 / Gamma-toxin target 7 / HAT-associated protein 1


Mass: 42230.098 Da / Num. of mol.: 1 / Fragment: UNP residues 67-438
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: ELP4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02884
#2: Protein Elongator complex protein 5 / / Gamma-toxin target 5 / HAT-associated protein 2 / Protein IKI1


Mass: 27623.412 Da / Num. of mol.: 1 / Fragment: UNP residues 1-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: ELP5 / Production host: Escherichia coli (E. coli) / References: UniProt: P38874
#3: Protein Elongator complex protein 6 / Gamma-toxin target 6 / HAT-associated protein 3


Mass: 30900.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: ELP6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04868
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-tris propane, 0.8M DL-Malic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→39.8 Å / Num. all: 32981 / Num. obs: 32701 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 51.22 Å2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.606→39.765 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8415 / SU ML: 0.28 / σ(F): 0 / Phase error: 22.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 1661 5.08 %RANDOM
Rwork0.1737 ---
obs0.1762 32701 99.1 %-
all-32981 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.804 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 164.03 Å2 / Biso mean: 62.0096 Å2 / Biso min: 18.76 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.606→39.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5483 0 0 19 5502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095589
X-RAY DIFFRACTIONf_angle_d1.1457619
X-RAY DIFFRACTIONf_chiral_restr0.078926
X-RAY DIFFRACTIONf_plane_restr0.005968
X-RAY DIFFRACTIONf_dihedral_angle_d16.2341991
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6056-2.69870.28831530.21752963311697
2.6987-2.80670.28581680.20633040320898
2.8067-2.93440.3021550.20673093324899
2.9344-3.08910.28461650.201430983263100
3.0891-3.28250.25341780.19283081325999
3.2825-3.53580.22311670.171731053272100
3.5358-3.89140.23051580.161531303288100
3.8914-4.45380.20111570.140631623319100
4.4538-5.60880.18691930.145431453338100
5.6088-39.76930.20231670.19653223339099
Refinement TLS params.Method: refined / Origin x: 86.2584 Å / Origin y: -23.2347 Å / Origin z: -22.7508 Å
111213212223313233
T0.2302 Å2-0.0298 Å20.0029 Å2-0.1032 Å20.0533 Å2--0.1997 Å2
L1.3436 °2-0.1694 °20.0498 °2-0.582 °2-0.2168 °2--1.0505 °2
S0.0072 Å °0.0396 Å °0.2359 Å °-0.1508 Å °-0.0238 Å °0.0089 Å °0.1413 Å °-0.0723 Å °0.0021 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 67:367 OR RESID 501:502 ) ) OR ( CHAIN C AND ( RESID 2:272 OR RESID 301:313 ) ) OR ( CHAIN B AND ( RESID 7:234 OR RESID 301:304 ) )A67 - 367
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 67:367 OR RESID 501:502 ) ) OR ( CHAIN C AND ( RESID 2:272 OR RESID 301:313 ) ) OR ( CHAIN B AND ( RESID 7:234 OR RESID 301:304 ) )A501 - 502
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 67:367 OR RESID 501:502 ) ) OR ( CHAIN C AND ( RESID 2:272 OR RESID 301:313 ) ) OR ( CHAIN B AND ( RESID 7:234 OR RESID 301:304 ) )C2 - 272
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 67:367 OR RESID 501:502 ) ) OR ( CHAIN C AND ( RESID 2:272 OR RESID 301:313 ) ) OR ( CHAIN B AND ( RESID 7:234 OR RESID 301:304 ) )C301 - 313
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 67:367 OR RESID 501:502 ) ) OR ( CHAIN C AND ( RESID 2:272 OR RESID 301:313 ) ) OR ( CHAIN B AND ( RESID 7:234 OR RESID 301:304 ) )B7 - 234
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 67:367 OR RESID 501:502 ) ) OR ( CHAIN C AND ( RESID 2:272 OR RESID 301:313 ) ) OR ( CHAIN B AND ( RESID 7:234 OR RESID 301:304 ) )B301 - 304

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