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- PDB-2bv3: Crystal structure of a mutant elongation factor G trapped with a ... -

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Basic information

Entry
Database: PDB / ID: 2bv3
TitleCrystal structure of a mutant elongation factor G trapped with a GTP analogue
ComponentsELONGATION FACTOR GEF-G
KeywordsELONGATION FACTOR / SWITCH II / GTP-BINDING / TRANSLATION MUTATION THR84ALA / PROTEIN BIOSYNTHESIS
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Elongation factor G
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHansson, S. / Singh, R. / Gudkov, A.T. / Liljas, A. / Logan, D.T.
Citation
Journal: FEBS Lett. / Year: 2005
Title: Crystal Structure of a Mutant Elongation Factor G Trapped with a GTP Analogue.
Authors: Hansson, S. / Singh, R. / Gudkov, A.T. / Liljas, A. / Logan, D.T.
#1: 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.
#2: Journal: EMBO J / Year: 1994
Title: Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus.
Authors: A AEvarsson / E Brazhnikov / M Garber / J Zheltonosova / Y Chirgadze / S al-Karadaghi / L A Svensson / A Liljas /
Abstract: The crystal structure of Thermus thermophilus elongation factor G without guanine nucleotide was determined to 2.85 A. This GTPase has five domains with overall dimensions of 50 x 60 x 118 A. The GTP ...The crystal structure of Thermus thermophilus elongation factor G without guanine nucleotide was determined to 2.85 A. This GTPase has five domains with overall dimensions of 50 x 60 x 118 A. The GTP binding domain has a core common to other GTPases with a unique subdomain which probably functions as an intrinsic nucleotide exchange factor. Domains I and II are homologous to elongation factor Tu and their arrangement, both with and without GDP, is more similar to elongation factor Tu in complex with a GTP analogue than with GDP. Domains III and V show structural similarities to ribosomal proteins. Domain IV protrudes from the main body of the protein and has an extraordinary topology with a left-handed cross-over connection between two parallel beta-strands.
#3: 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.
#4: Journal: J.Mol.Biol. / Year: 2000
Title: Structure of a Mutant EF-G Reveals Domain III and Possibly the Fusidic Acid Binding Site
Authors: Laurberg, M. / Kristensen, O. / Martemyanov, K. / Gudkov, A.T. / Nagaev, I. / Hughes, D. / Liljas, A.
#5: Journal: J.Biol.Chem. / Year: 2001
Title: Mutations in the G-Domain of Elongation Factor G from Thermus Thermophilus Affect Both its Interaction with GTP and Fusidic Acid.
Authors: Martemyanov, K.A. / Liljas, A. / Yarunin, A.S. / Gudkov, A.T.
#6: Journal: J.Mol.Biol. / Year: 2005
Title: Structural Insights Into Fusidic Acid Resistance and Sensitivity in EF-G
Authors: Hansson, S. / Singh, R. / Gudkov, A.T. / Liljas, A. / Logan, D.T.
History
DepositionJun 22, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)77,3033
Polymers76,7571
Non-polymers5472
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.990, 103.340, 118.910
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: 76756.836 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Plasmid: PET13A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13551
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 84 TO ALA

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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 Å3/Da / Density % sol: 58.6 %
Crystal growpH: 7.3
Details: 17 % PEG8000, 10 MM MGCL2, 100 MM GDPNP, 46 MM TRIS, 100 MM HEPES, pH 7.30

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9787
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 16, 2004 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.5→26.9 Å / Num. obs: 30656 / % possible obs: 96.5 % / Observed criterion σ(I): 2.5 / Redundancy: 7.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.5
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.7 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BM0

2bm0


Resolution: 2.5→17.43 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.905 / SU B: 25.057 / SU ML: 0.246 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.394 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-6, 42-60, 689-691 ARE MISSING.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1572 5.1 %RANDOM
Rwork0.202 ---
obs0.205 29084 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2---1.08 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.5→17.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4848 0 33 157 5038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224974
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9856754
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.135628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24423.894208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.26415841
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9231536
X-RAY DIFFRACTIONr_chiral_restr0.0940.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023726
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.22116
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23366
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2217
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.08923216
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.83335071
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.91321969
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.37431683
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.428 65
Rwork0.326 1124
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)
11.52010.7143-0.90980.8763-0.32563.6090.0231-0.1465-0.0747-0.019-0.2591-0.1853-0.49430.48390.236-0.0368-0.0893-0.0607-0.18130.04010.1855-15.39536.81143.329
22.86091.4063-1.90264.4935-1.80576.7768-0.00180.18110.12970.083-0.3046-0.4272-0.83540.64260.30640.2117-0.1143-0.1567-0.09570.12740.1679-9.65652.18419.149
316.864.07913.43718.33315.90932.18711.29581.2556-1.673-1.0358-1.0103-0.82690.4089-1.778-0.28550.49820.08440.07760.62910.15530.404119.15848.00528.747
44.03991.4299-2.24981.1729-0.51994.2621-0.2471-0.451-0.42640.33760.20990.03910.20240.70070.0372-0.14610.15670.0431-0.16360.10920.218438.40565.67224.392
511.42617.3376-7.28997.4801-3.64237.34210.6709-1.0538-0.23840.394-0.7222-0.1048-0.2727-0.78540.05130.0801-0.09940.00660.38890.26470.433811.1551.16150.58
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 284
2X-RAY DIFFRACTION2A285 - 400
3X-RAY DIFFRACTION3A401 - 483
4X-RAY DIFFRACTION4A484 - 605
5X-RAY DIFFRACTION4A674 - 691
6X-RAY DIFFRACTION5A606 - 673

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