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- PDB-2efg: TRANSLATIONAL ELONGATION FACTOR G COMPLEXED WITH GDP -

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Basic information

Entry
Database: PDB / ID: 2efg
TitleTRANSLATIONAL ELONGATION FACTOR G COMPLEXED WITH GDP
Components
  • PROTEIN (ELONGATION FACTOR G DOMAIN 3)
  • PROTEIN (ELONGATION FACTOR G)
KeywordsPROTEIN BINDING / ELONGATION FACTOR / TRANSLOCASE / RIBOSOME / ELONGATION / TRANSLATION / PROTEIN SYNT FACTOR / GTPASE / GTP BINDING / GUANOSINE NUCLEOTIDE BINDING
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
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 ...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 / Elongation factor G
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.6 Å
AuthorsCzworkowski, J. / Wang, J. / Steitz, T.A. / Moore, P.B.
Citation
Journal: EMBO J. / Year: 1994
Title: The crystal structure of elongation factor G complexed with GDP, at 2.7 A resolution.
Authors: Czworkowski, J. / Wang, J. / Steitz, T.A. / Moore, P.B.
#1: Journal: Structure / Year: 1996
Title: The Structure of Elongation Factor G in Complex with GDP: Conformational Flexibility and Nucleotide Exchange
Authors: al-Karadaghi, S. / Aevarsson, A. / Garber, M. / Zheltonosova, J. / Liljas, A.
#2: Journal: Embo J. / Year: 1994
Title: Three-Dimensional Structure of the Ribosomal Translocase: Elongation Factor G from Thermus thermophilus
Authors: Aevarsson, A. / Brazhnikov, E. / Garber, M. / Zheltonosova, J. / Chirgadze, Y. / al-Karadaghi, S. / Svensson, L.A. / Liljas, A.
History
DepositionSep 23, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 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: PROTEIN (ELONGATION FACTOR G)
B: PROTEIN (ELONGATION FACTOR G DOMAIN 3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9143
Polymers84,4702
Non-polymers4431
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.269, 106.224, 115.447
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 PROTEIN (ELONGATION FACTOR G) / EF-G


Mass: 76963.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P13551, UniProt: Q5SHN5*PLUS
#2: Protein PROTEIN (ELONGATION FACTOR G DOMAIN 3) / EF-G


Mass: 7507.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#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
#4: 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.8
Details: 18% W/V PEG8000, 20MM TRIS-HCL, 20MM AMMONIUM ACETATE, 2MM DTT, 1MM SODIUM AZIDE, 1MM GDP, pH 7.8, VAPOR DIFFUSION, HANGING DROP
Crystal
*PLUS
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116-20 %(w/v)PEG80001reservoir
220 mMTris-HCl1reservoir
32 mMdithiothreitol1reservoir
41 mMGDP1reservoir
51 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 29, 1992 / Details: DOUBLE FOCUSING MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 29278 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 61.6 Å2 / Rsym value: 0.7 / Net I/σ(I): 21
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.95 / Rsym value: 0.907 / % possible all: 97.5

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MIRAS
Starting model: PDB ENTRY 1EFG

1efg


Resolution: 2.6→80 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 7320367.21 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. REFINEMENT WAS THE MAXIMUM TARGET USING AMPLITUDES; REFINEMENT OF THIS STRUCTURE, LEADING TO ENTRY 1EFG, EMPLO PROGRAM X-PLOR
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2685 9.9 %RANDOM
Rwork0.221 ---
obs0.221 27063 90.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.28 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso mean: 60.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.6→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4807 0 28 21 4856
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it8.961.5
X-RAY DIFFRACTIONc_mcangle_it9.912
X-RAY DIFFRACTIONc_scbond_it6.062
X-RAY DIFFRACTIONc_scangle_it8.432.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.433 401 10.5 %
Rwork0.382 3408 -
obs--77.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3EFGGDP2-GDP.PAREFGGDP2-GDP.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 80 Å / σ(F): 0 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 60.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.433 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.382

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