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- PDB-4m1k: Crystal structure of elongation factor G (EFG) -

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Basic information

Entry
Database: PDB / ID: 4m1k
TitleCrystal structure of elongation factor G (EFG)
ComponentsElongation factor GEF-G
KeywordsTRANSLATION / Elongation factor G
Function / homology
Function and homology information


translational elongation / translation elongation factor activity / GDP binding / ribosome binding / GTPase activity / GTP binding / magnesium ion binding / cytoplasm
Similarity search - Function
Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / : / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal Protein S5; domain 2 - #10 / Translation elongation factor EFG/EF2, domain IV ...Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / : / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal Protein S5; domain 2 - #10 / 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 / Translation factors / EF-G domain III/V-like / Ribosomal Protein S5; domain 2 / 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. / Elongation Factor Tu (Ef-tu); domain 3 / 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 / Alpha-Beta Plaits / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor G
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.952 Å
AuthorsLiu, G. / Dong, J. / Gong, W. / Qin, Y.
CitationJournal: To be published
Title: Crystal structure of elongation factor G (EFG)
Authors: Liu, G. / Dong, J. / Gong, W. / Qin, Y.
History
DepositionAug 2, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4303
Polymers76,9621
Non-polymers4682
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.989, 86.767, 123.118
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 G / EF-G / EF-G


Mass: 76962.133 Da / Num. of mol.: 1 / Mutation: Q500L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: fusA, fus / Production host: Escherichia coli (E. coli) / References: UniProt: P13551
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


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

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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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5mM Tris-HCl (pH 7.6), 10mM MgCl2, 5mM GDP, 20-23% PEG8000, 0.1M Tris-Cl PH7.5-7.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 10, 2012
RadiationMonochromator: 0 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. all: 17686 / Num. obs: 17685 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.95→3.06 Å / Rmerge(I) obs: 0.549 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CNSrefinement
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FNM

1fnm


Resolution: 2.952→37.995 Å / SU ML: 0.73 / σ(F): 1.34 / Phase error: 28.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2919 898 5.09 %RANDOM
Rwork0.1936 ---
obs0.1985 17639 99.73 %-
all-17685 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.299 Å2 / ksol: 0.305 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1725 Å20 Å2-0 Å2
2--6.1568 Å20 Å2
3----7.3293 Å2
Refinement stepCycle: LAST / Resolution: 2.952→37.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5104 0 29 0 5133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095229
X-RAY DIFFRACTIONf_angle_d1.2277094
X-RAY DIFFRACTIONf_dihedral_angle_d20.0441984
X-RAY DIFFRACTIONf_chiral_restr0.076810
X-RAY DIFFRACTIONf_plane_restr0.005920
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9518-3.13670.35331560.2464268999
3.1367-3.37870.3531440.23692751100
3.3787-3.71850.37991560.20912753100
3.7185-4.2560.29091540.18852787100
4.256-5.35970.23271500.1542798100
5.3597-37.99760.24281380.18662963100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.83380.3907-0.22510.5510.29831.24760.1264-0.01870.00840.22140.007-0.06050.00410.04550.00740.1687-0.032-0.0120.09340.02030.0911-16.6375-10.7321-15.0799
20.44240.2506-0.08750.291-0.23640.4604-0.00140.08030.0673-0.1151-0.01140.09150.04520.1316-0.00110.1227-0.02180.02590.31120.04210.1866-8.4492.9069-40.5305
30.9306-0.2350.32120.2275-0.10870.11170.32580.2423-0.0898-0.1618-0.2405-0.03710.04140.10010.12030.12890.01720.04280.2096-0.04210.16932.53381.9588-38.7235
40.05930.0224-0.00860.1545-0.09440.0581-0.11540.29940.1403-0.0835-0.4741-0.4584-0.09720.1511-0.00580.6357-0.133-0.06720.6742-0.04210.605819.5958-7.2597-40.4497
50.41310.08450.06110.4507-0.11680.38190.0493-0.12860.0084-0.10210.01030.0629-0.0648-0.09330.01490.09550.0237-0.04150.16260.02510.263433.94355.3713-38.5207
60.52360.10160.13830.25640.10860.13020.2709-0.2217-0.07790.0873-0.0992-0.0042-0.04620.07830.06620.1155-0.15210.05590.19580.18210.008125.02794.3241-21.0043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESSEQ 6:289)
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESSEQ 290:366)
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESSEQ 367:418)
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESSEQ 419:455)
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESSEQ 456:562)
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESSEQ 563:688)

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