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- PDB-5jbq: EF-TU (ESCHERICHIA COLI) IN COMPLEX WITH THIOMURACIN ANALOG -

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Basic information

Entry
Database: PDB / ID: 5jbq
TitleEF-TU (ESCHERICHIA COLI) IN COMPLEX WITH THIOMURACIN ANALOG
Components
  • Elongation factor Tu 1EF-Tu
  • THIOMURACIN ANALOG
KeywordsRNA BINDING PROTEIN/ANTIMICROBIAL / natural product inhibitor / elongation factor / RNA BINDING PROTEIN-ANTIMICROBIAL complex
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / translational elongation / guanosine tetraphosphate binding / translation elongation factor activity / response to antibiotic / GTPase activity / GTP binding / RNA binding / plasma membrane / 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
GUANOSINE-5'-DIPHOSPHATE / Elongation factor Tu 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.006 Å
AuthorsPalestrant, D. / Stams, T.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Antibacterial and Solubility Optimization of Thiomuracin A.
Authors: LaMarche, M.J. / Leeds, J.A. / Brewer, J. / Dean, K. / Ding, J. / Dzink-Fox, J. / Gamber, G. / Jain, A. / Kerrigan, R. / Krastel, P. / Lee, K. / Lombardo, F. / McKenney, D. / Neckermann, G. ...Authors: LaMarche, M.J. / Leeds, J.A. / Brewer, J. / Dean, K. / Ding, J. / Dzink-Fox, J. / Gamber, G. / Jain, A. / Kerrigan, R. / Krastel, P. / Lee, K. / Lombardo, F. / McKenney, D. / Neckermann, G. / Osborne, C. / Palestrant, D. / Patane, M.A. / Rann, E.M. / Robinson, Z. / Schmitt, E. / Stams, T. / Tiamfook, S. / Yu, D. / Whitehead, L.
History
DepositionApr 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / entity_poly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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.ptnr2_symmetry / _struct_conn_type.id / _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

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Assembly

Deposited unit
A: Elongation factor Tu 1
B: THIOMURACIN ANALOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4326
Polymers44,8442
Non-polymers5884
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-40 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.350, 125.340, 45.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-402-

MG

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Elongation factor Tu 1 / EF-Tu / EF-Tu 1 / Bacteriophage Q beta RNA-directed RNA polymerase subunit III / P-43


Mass: 43340.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: tufA, b3339, JW3301 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CE47
#2: Protein/peptide THIOMURACIN ANALOG


Mass: 1503.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 228 molecules

#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.2M MgSO4, 18% PEG3350, 100mM Tris Cryo 20% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Apr 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.006→42.69 Å / Num. obs: 31079 / % possible obs: 98.5 % / Redundancy: 4.7 % / Biso Wilson estimate: 25.55 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.7
Reflection shellResolution: 2.006→2.012 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.2 / % possible all: 66.2

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
SCALAdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.006→42.69 Å / Cor.coef. Fo:Fc: 0.9274 / Cor.coef. Fo:Fc free: 0.8954 / SU R Cruickshank DPI: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.192 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.168
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 1507 4.88 %RANDOM
Rwork0.2045 ---
obs0.2069 30901 98.63 %-
Displacement parametersBiso mean: 27.36 Å2
Baniso -1Baniso -2Baniso -3
1-5.398 Å20 Å20 Å2
2---2.564 Å20 Å2
3----2.834 Å2
Refine analyzeLuzzati coordinate error obs: 0.268 Å
Refinement stepCycle: LAST / Resolution: 2.006→42.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3027 0 125 224 3376
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013218HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.164373HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1136SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes483HARMONIC5
X-RAY DIFFRACTIONt_it3218HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion18.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion421SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3744SEMIHARMONIC4
LS refinement shellResolution: 2.01→2.08 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2352 139 5.53 %
Rwork0.2235 2376 -
all0.2242 2515 -
obs--88.99 %

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