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- PDB-3u6k: Ef-tu (escherichia coli) in complex with nvp-ldk733 -

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Basic information

Entry
Database: PDB / ID: 3u6k
TitleEf-tu (escherichia coli) in complex with nvp-ldk733
Components
  • Elongation factor Tu 1EF-Tu
  • Thiocillin GE2270 analogue NVP-LDK733
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-LDK733 / GUANOSINE-5'-DIPHOSPHATE / Elongation factor Tu 1 / Thiocillin GE2270
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsPalestrant, D.J.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Antibacterial optimization of 4-aminothiazolyl analogues of the natural product GE2270 A: identification of the cycloalkylcarboxylic acids.
Authors: LaMarche, M.J. / Leeds, J.A. / Amaral, K. / Brewer, J.T. / Bushell, S.M. / Dewhurst, J.M. / Dzink-Fox, J. / Gangl, E. / Goldovitz, J. / Jain, A. / Mullin, S. / Neckermann, G. / Osborne, C. / ...Authors: LaMarche, M.J. / Leeds, J.A. / Amaral, K. / Brewer, J.T. / Bushell, S.M. / Dewhurst, J.M. / Dzink-Fox, J. / Gangl, E. / Goldovitz, J. / Jain, A. / Mullin, S. / Neckermann, G. / Osborne, C. / Palestrant, D. / Patane, M.A. / Rann, E.M. / Sachdeva, M. / Shao, J. / Tiamfook, S. / Whitehead, L. / Yu, D.
History
DepositionOct 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Structure summary
Revision 1.2Dec 12, 2012Group: Other
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 / database_2 / entity_poly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongation factor Tu 1
B: Elongation factor Tu 1
C: Thiocillin GE2270 analogue NVP-LDK733
D: Thiocillin GE2270 analogue NVP-LDK733
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4718
Polymers89,5364
Non-polymers9354
Water2,612145
1
A: Elongation factor Tu 1
C: Thiocillin GE2270 analogue NVP-LDK733
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2364
Polymers44,7682
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-22 kcal/mol
Surface area17840 Å2
MethodPISA
2
B: Elongation factor Tu 1
D: Thiocillin GE2270 analogue NVP-LDK733
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2364
Polymers44,7682
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-23 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.372, 82.216, 129.900
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 Tu 1 / EF-Tu / EF-Tu 1 / P-43


Mass: 43324.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tufA, b3339, JW3301 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P0CE47
#2: Protein/peptide Thiocillin GE2270 analogue NVP-LDK733


Type: Thiopeptide / Class: Antibiotic / Mass: 1443.649 Da / Num. of mol.: 2 / Source method: obtained synthetically
References: UniProt: Q7M0J8, Thiocillin GE2270 analogue NVP-LDK733
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 HEPES PH 7.5, 0.3 MGCL2, 21% PEG3350, 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: Aug 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 32122 / Num. obs: 32122 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.45→2.54 Å / % possible all: 99.8

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→43.04 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.298 1590 random
Rwork0.224 --
all0.228 30572 -
obs0.228 30572 -
Refinement stepCycle: LAST / Resolution: 2.45→43.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6108 0 58 145 6311
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.2
LS refinement shellResolution: 2.45→2.6 Å / Num. reflection obs: 4305

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