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- PDB-2bm1: Ribosomal elongation factor G (EF-G) Fusidic acid resistant mutan... -

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Basic information

Entry
Database: PDB / ID: 2bm1
TitleRibosomal elongation factor G (EF-G) Fusidic acid resistant mutant G16V
ComponentsELONGATION FACTOR G
KeywordsELONGATION FACTOR / SWITCH II / GTP-BINDING / MUTATION GLY16VAL / PROTEIN BIOSYNTHESIS / TRANSLATION
Function / homology
Function and homology information


ribosome disassembly / 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 / Ribosomal Protein S5; domain 2 - #10 / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation factors ...Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Ribosomal Protein S5; domain 2 - #10 / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation factors / 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 / 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 / Elongation Factor Tu (Ef-tu); domain 3 / 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 nucleotide triphosphate hydrolases / Alpha-Beta Plaits / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHansson, S. / Singh, R. / Gudkov, A.T. / Liljas, A. / Logan, D.T.
Citation
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.
#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.
History
DepositionMar 9, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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 / _struct_conn.ptnr2_symmetry
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. 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)77,4873
Polymers77,0191
Non-polymers4682
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.300, 89.700, 114.900
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


Mass: 77019.180 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-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: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 16 TO VAL

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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: 2.6 Å3/Da / Density % sol: 51.5 %
Crystal growpH: 7.3
Details: 17 % PEG8000 100 MM HEPES 46 MM TRIS-HCL PH 7.3 10 MM MAGNESIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.6→28 Å / Num. obs: 24149 / % possible obs: 98.2 % / Observed criterion σ(I): 3 / Redundancy: 8.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.2 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BM0

2bm0


Resolution: 2.6→28 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.853 / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.297 -5 %RANDOM
Rwork0.22 ---
obs0.22 23255 98.2 %-
Displacement parametersBiso mean: 60.99 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5167 0 29 62 5258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225412
X-RAY DIFFRACTIONr_bond_other_d0.0020.025065
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9787335
X-RAY DIFFRACTIONr_angle_other_deg0.931311783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.55673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.2833
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025957
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021040
X-RAY DIFFRACTIONr_nbd_refined0.2150.21196
X-RAY DIFFRACTIONr_nbd_other0.2170.26257
X-RAY DIFFRACTIONr_nbtor_refined0.180.22554
X-RAY DIFFRACTIONr_nbtor_other0.090.23545
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2126
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2790.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8191.53356
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50625451
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.64532056
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9244.51884
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

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