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- PDB-1ob5: T. aquaticus elongation factor EF-Tu complexed with the antibioti... -

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Basic information

Entry
Database: PDB / ID: 1ob5
TitleT. aquaticus elongation factor EF-Tu complexed with the antibiotic enacyloxin IIa, a GTP analog, and Phe-tRNA
Components
  • ELONGATION FACTOR TUEF-Tu
  • TRANSFER-RNA, PHE
KeywordsHYDROLASE / GTPASE / TRANSLATION ELONGATION FACTOR / TRANSFER RNA / GTP-BINDING / NUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS
Function / homology
Function and homology information


translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 ...Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / 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 / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ENACYLOXIN IIA / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / RNA / RNA (> 10) / Elongation factor Tu
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
SACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsDahlberg, C. / Nielsen, R.C. / Parmeggiani, A. / Nyborg, J. / Nissen, P.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Enacyloxin Iia Pinpoints a Binding Pocket of Elongation Factor TU for Development of Novel Antibiotics.
Authors: Parmeggiani, A. / Krab, I.M. / Watanabe, T. / Nielsen, R.C. / Dahlberg, C. / Nyborg, J. / Nissen, P.
History
DepositionJan 24, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2005Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jul 24, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_validate_polymer_linkage / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_polymer_linkage / struct_conn / struct_conn_type / struct_site
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 / _pdbx_validate_polymer_linkage.auth_atom_id_1 / _pdbx_validate_polymer_linkage.dist / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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 TU
B: TRANSFER-RNA, PHE
C: ELONGATION FACTOR TU
D: TRANSFER-RNA, PHE
E: ELONGATION FACTOR TU
F: TRANSFER-RNA, PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,95615
Polymers210,2086
Non-polymers3,7479
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)212.570, 122.330, 135.680
Angle α, β, γ (deg.)90.00, 121.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ELONGATION FACTOR TU / EF-Tu / EF-TU


Mass: 44742.980 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS AQUATICUS (bacteria) / Description: TUF-A GENE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01698, EC: 3.6.1.48
#2: RNA chain TRANSFER-RNA, PHE


Mass: 25326.479 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: SIGMA-ALDRICH COMPOUND / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ENX / ENACYLOXIN IIA


Mass: 702.616 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H45Cl2NO11
Compound detailsPROMOTES THE GTP-DEPENDENT BINDING OF AMINOACYL-TRNA TO THE A-SITE OF RIBOSOMES DURING PROTEIN BIOSYNTHESIS.

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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: 3.6 Å3/Da / Density % sol: 64 %
Crystal growpH: 6.8
Details: 1.8M AMMONIUM SULPHATE, 10 MM MAGNESIUM CHLORIDE,20 MM TRIS-MES, PH 6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.802
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 4, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.802 Å / Relative weight: 1
ReflectionResolution: 3.33→30 Å / Num. obs: 48311 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 68.3 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12
Reflection shellResolution: 3.3→3.38 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 4.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LD1

1ld1
PDB Unreleased entry


Resolution: 3.1→29.54 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 8253666.21 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1581 2.9 %RANDOM
Rwork0.2796 ---
obs0.2796 53684 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.7579 Å2 / ksol: 0.290638 e/Å3
Displacement parametersBiso mean: 76.5 Å2
Baniso -1Baniso -2Baniso -3
1--7.972 Å20 Å213.061 Å2
2---27.052 Å20 Å2
3---35.024 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.54 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 3.1→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9318 4989 240 0 14547
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.46
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.7871.5
X-RAY DIFFRACTIONc_mcangle_it9.4742
X-RAY DIFFRACTIONc_scbond_it8.1212
X-RAY DIFFRACTIONc_scangle_it11.7422.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2TRNAPHE-MULTI2.PARAM
X-RAY DIFFRACTION3LIGANDS.PAR
X-RAY DIFFRACTION4MG.PAR

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