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- PDB-5h7j: Crystal structure of Elongation factor 2 -

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Basic information

Entry
Database: PDB / ID: 5h7j
TitleCrystal structure of Elongation factor 2
ComponentsElongation factor 2EEF2
KeywordsTRANSLATION / Elongation factor / Protein biosynthesis / GTP-binding
Function / homology
Function and homology information


translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Translation elongation factor EFG/EF2, archaeal / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like ...Translation elongation factor EFG/EF2, archaeal / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Elongation factor 2
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTanzawa, T. / Kato, K. / Uchiumi, T. / Yao, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science26650013 Japan
Japan Society for the Promotion of Science24370073 Japan
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: The C-terminal helix of ribosomal P stalk recognizes a hydrophobic groove of elongation factor 2 in a novel fashion
Authors: Tanzawa, T. / Kato, K. / Girodat, D. / Ose, T. / Kumakura, Y. / Wieden, H.J. / Uchiumi, T. / Tanaka, I. / Yao, M.
History
DepositionNov 18, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongation factor 2
B: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,4003
Polymers167,8782
Non-polymers5211
Water3,693205
1
A: Elongation factor 2


Theoretical massNumber of molelcules
Total (without water)83,9391
Polymers83,9391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area31260 Å2
MethodPISA
2
B: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4602
Polymers83,9391
Non-polymers5211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-3 kcal/mol
Surface area31030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.216, 116.131, 189.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Elongation factor 2 / EEF2 / EF-2


Mass: 83939.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Strain: OT3 / Gene: fusA / Plasmid: pET26M / Production host: Escherichia coli (E. coli) / References: UniProt: O59521
#2: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.76 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 10 % PEG 6000, 0.1 M MES-NaOH

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 82481 / % possible obs: 99.2 % / Redundancy: 5.13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.23
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 5.15 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3.8 / CC1/2: 0.889 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOLREPphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→39.586 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.67
RfactorNum. reflection% reflection
Rfree0.2567 4129 5.01 %
Rwork0.2151 --
obs0.2172 82476 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10880 0 32 205 11117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111122
X-RAY DIFFRACTIONf_angle_d1.3215037
X-RAY DIFFRACTIONf_dihedral_angle_d16.5124284
X-RAY DIFFRACTIONf_chiral_restr0.0511698
X-RAY DIFFRACTIONf_plane_restr0.0051940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2997-2.32680.30551200.26772564X-RAY DIFFRACTION94
2.3268-2.35520.3221460.26522697X-RAY DIFFRACTION100
2.3552-2.3850.30561260.26142669X-RAY DIFFRACTION100
2.385-2.41630.31841450.25492709X-RAY DIFFRACTION100
2.4163-2.44940.30921600.26352633X-RAY DIFFRACTION100
2.4494-2.48440.29581690.26122687X-RAY DIFFRACTION100
2.4844-2.52150.34071440.24922688X-RAY DIFFRACTION100
2.5215-2.56090.38541550.26592709X-RAY DIFFRACTION100
2.5609-2.60290.32551280.26062666X-RAY DIFFRACTION100
2.6029-2.64780.32091050.25772743X-RAY DIFFRACTION100
2.6478-2.69590.32121400.26072709X-RAY DIFFRACTION100
2.6959-2.74770.31541460.26222664X-RAY DIFFRACTION100
2.7477-2.80380.33331470.25182727X-RAY DIFFRACTION100
2.8038-2.86470.29271380.25492695X-RAY DIFFRACTION100
2.8647-2.93140.33731360.25482721X-RAY DIFFRACTION100
2.9314-3.00460.31431320.26652727X-RAY DIFFRACTION100
3.0046-3.08590.34681560.2522678X-RAY DIFFRACTION100
3.0859-3.17660.29421280.24632714X-RAY DIFFRACTION100
3.1766-3.27910.30951600.2412692X-RAY DIFFRACTION100
3.2791-3.39620.28491500.23992731X-RAY DIFFRACTION100
3.3962-3.53210.25361510.23272714X-RAY DIFFRACTION100
3.5321-3.69280.25921410.21362716X-RAY DIFFRACTION100
3.6928-3.88730.24611530.20512726X-RAY DIFFRACTION100
3.8873-4.13060.22551350.19372711X-RAY DIFFRACTION99
4.1306-4.44920.19441340.17492766X-RAY DIFFRACTION99
4.4492-4.89620.19771370.16322727X-RAY DIFFRACTION99
4.8962-5.6030.21651520.18072744X-RAY DIFFRACTION99
5.603-7.05260.21481600.19952767X-RAY DIFFRACTION99
7.0526-39.59190.20021350.17592653X-RAY DIFFRACTION90

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