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- PDB-3u2q: EF-Tu (Escherichia coli) in complex with NVP-LFF571 -

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Basic information

Entry
Database: PDB / ID: 3u2q
TitleEF-Tu (Escherichia coli) in complex with NVP-LFF571
Components
  • Elongation factor Tu 1EF-Tu
  • Thiocillin GE2270 analogue NVP-LFF571
Keywordstranslation factor/antibiotic / translation factor-antibiotic complex
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / killing of cells of another organism / defense response to bacterium / response to antibiotic / GTPase activity / GTP binding / RNA binding ...guanyl-nucleotide exchange factor complex / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / killing of cells of another organism / defense response to bacterium / response to antibiotic / GTPase activity / GTP binding / RNA binding / extracellular region / 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
Thiocillin GE2270 analogue NVP-LFF571 / GUANOSINE-5'-DIPHOSPHATE / Elongation factor Tu 1 / Thiocillin GE2270
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPalestrant, D.J.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Discovery of LFF571: an investigational agent for Clostridium difficile infection.
Authors: LaMarche, M.J. / Leeds, J.A. / Amaral, A. / Brewer, J.T. / Bushell, S.M. / Deng, G. / Dewhurst, J.M. / Ding, J. / Dzink-Fox, J. / Gamber, G. / Jain, A. / Lee, K. / Lee, L. / Lister, T. / ...Authors: LaMarche, M.J. / Leeds, J.A. / Amaral, A. / Brewer, J.T. / Bushell, S.M. / Deng, G. / Dewhurst, J.M. / Ding, J. / Dzink-Fox, J. / Gamber, G. / Jain, A. / Lee, K. / Lee, L. / Lister, T. / McKenney, D. / Mullin, S. / Osborne, C. / Palestrant, D. / Patane, M.A. / Rann, E.M. / Sachdeva, M. / Shao, J. / Tiamfook, S. / Trzasko, A. / Whitehead, L. / Yifru, A. / Yu, D. / Yan, W. / Zhu, Q.
History
DepositionOct 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other
Revision 2.0Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor Tu 1
B: Thiocillin GE2270 analogue NVP-LFF571
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3364
Polymers44,8682
Non-polymers4682
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-22 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.303, 132.473, 37.433
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-443-

HOH

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Components

#1: Protein Elongation factor Tu 1 / EF-Tu / EF-Tu 1 / P-43


Mass: 43324.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tufA, b3339, JW3301 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CE47
#2: Protein/peptide Thiocillin GE2270 analogue NVP-LFF571


Type: Thiopeptide / Class: Antibiotic / Mass: 1543.765 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: UniProt: Q7M0J8, Thiocillin GE2270 analogue NVP-LFF571
#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.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE GE2270A-LIKE ANTIBIOTIC COMPOUND IS REPRESENTED AS POLYMER. THE FIRST 11 RESIDUES OF THE ...THE GE2270A-LIKE ANTIBIOTIC COMPOUND IS REPRESENTED AS POLYMER. THE FIRST 11 RESIDUES OF THE ANTIBIOTIC ARE IDENTICAL TO THE CORRESPONDING RESIDUES IN GE2270A, WITH ONLY THE LAST RESIDUE MODIFIED
Sequence detailsTHE GE2270A-LIKE ANTIBIOTIC COMPOUND IS REPRESENTED AS POLYMER. THE FIRST 11 RESIDUES OF THE ...THE GE2270A-LIKE ANTIBIOTIC COMPOUND IS REPRESENTED AS POLYMER. THE FIRST 11 RESIDUES OF THE ANTIBIOTIC ARE IDENTICAL TO THE CORRESPONDING RESIDUES IN GE2270A, WITH ONLY THE LAST RESIDUE MODIFIED.

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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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.23
Details: 50mM Tris PH8, 50mM NaCl , pH 8.23, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 21, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 11365 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.79 / % possible all: 77.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNX2002refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1D8T

1d8t


Resolution: 2.7→39.02 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.315 582 random
Rwork0.233 --
all-11365 -
obs-11365 -
Refinement stepCycle: LAST / Resolution: 2.7→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3058 0 29 89 3176
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.007

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