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- PDB-5h7k: Crystal structure of Elongation factor 2 GDP-form -

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Basic information

Entry
Database: PDB / ID: 5h7k
TitleCrystal structure of Elongation factor 2 GDP-form
ComponentsElongation factor 2
KeywordsTRANSLATION / Elongation factor / Protein biosynthesis / GTP-binding
Function / homology
Function and homology information


translation elongation factor activity / cytosolic ribosome assembly / ribosome binding / ribonucleoprotein complex / GTPase activity / GTP binding / cytosol
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 / P-loop containing nucleotide triphosphate hydrolases / Ribosomal protein S5 domain 2-type fold / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor 2
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 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
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2622
Polymers44,8191
Non-polymers4431
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-6 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.159, 85.560, 114.422
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 / EF-2


Mass: 44818.926 Da / Num. of mol.: 1 / Fragment: UNP residues 1-386
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-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 10 % PEG 1000, 0.1 M MES-NaOH

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.599→50 Å / Num. obs: 65800 / % possible obs: 99.9 % / Redundancy: 7.25 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 19.07
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 7.24 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 2.52 / CC1/2: 0.82 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.599→47.559 Å / Cross valid method: FREE R-VALUE / Phase error: 18.24
RfactorNum. reflection% reflection
Rfree0.1979 2848 4.33 %
Rwork0.1712 --
obs0.1723 65789 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.599→47.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2883 0 28 408 3319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073092
X-RAY DIFFRACTIONf_angle_d1.1314197
X-RAY DIFFRACTIONf_dihedral_angle_d14.4181204
X-RAY DIFFRACTIONf_chiral_restr0.046471
X-RAY DIFFRACTIONf_plane_restr0.005545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5992-1.62680.25581510.22513085X-RAY DIFFRACTION99
1.6268-1.65640.25871300.22393093X-RAY DIFFRACTION100
1.6564-1.68820.22671610.22013116X-RAY DIFFRACTION100
1.6882-1.72270.25491230.20053111X-RAY DIFFRACTION100
1.7227-1.76010.2141320.19343135X-RAY DIFFRACTION100
1.7601-1.80110.22731580.19313100X-RAY DIFFRACTION100
1.8011-1.84610.21581400.18793091X-RAY DIFFRACTION100
1.8461-1.89610.2291390.18743120X-RAY DIFFRACTION100
1.8961-1.95180.23561410.22943131X-RAY DIFFRACTION100
1.9518-2.01480.20161410.16853122X-RAY DIFFRACTION100
2.0148-2.08690.20261410.16973139X-RAY DIFFRACTION100
2.0869-2.17040.2131410.1623121X-RAY DIFFRACTION100
2.1704-2.26920.24411410.19863128X-RAY DIFFRACTION99
2.2692-2.38880.18581420.16523139X-RAY DIFFRACTION100
2.3888-2.53850.19481420.16783162X-RAY DIFFRACTION100
2.5385-2.73450.20461420.16423143X-RAY DIFFRACTION100
2.7345-3.00960.17561420.1633196X-RAY DIFFRACTION100
3.0096-3.4450.1721430.16093191X-RAY DIFFRACTION100
3.445-4.33990.16551450.14333241X-RAY DIFFRACTION100
4.3399-47.57950.18261530.15883377X-RAY DIFFRACTION100

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