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- PDB-3u6b: Ef-tu (escherichia coli) in complex with nvp-ldi028 -

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Basic information

Entry
Database: PDB / ID: 3u6b
TitleEf-tu (escherichia coli) in complex with nvp-ldi028
Components
  • Elongation factor Tu 1EF-Tu
  • Thiocillin GE2270 analogue NVP-LDI028
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-LDI028 / GUANOSINE-5'-DIPHOSPHATE / Elongation factor Tu 1 / Thiocillin GE2270
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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 2.0Jan 29, 2020Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Polymer sequence / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity_poly / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.pdbx_synonyms / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

Downloads & links

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Assembly

Deposited unit
A: Elongation factor Tu 1
B: Elongation factor Tu 1
C: Thiocillin GE2270 analogue NVP-LDI028
D: Thiocillin GE2270 analogue NVP-LDI028
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4398
Polymers89,5044
Non-polymers9354
Water2,000111
1
A: Elongation factor Tu 1
D: Thiocillin GE2270 analogue NVP-LDI028
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2204
Polymers44,7522
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Elongation factor Tu 1
C: Thiocillin GE2270 analogue NVP-LDI028
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2204
Polymers44,7522
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.246, 100.376, 156.483
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-524-

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.: 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) / Strain (production host): BL21 (Star) / References: UniProt: P0CE47
#2: Protein/peptide Thiocillin GE2270 analogue NVP-LDI028 / EF-TU 1 / P-43 / EF-TU


Type: Thiopeptide / Class: Antibiotic / Mass: 1427.650 Da / Num. of mol.: 2 / Source method: obtained synthetically
References: UniProt: Q7M0J8, Thiocillin GE2270 analogue NVP-LDI028
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M AMMONIUM ACETATE, 22% PEG 3350, 0.1M BIS-TRIS PH6.5 , 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: Oct 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. all: 39701 / Num. obs: 39701 / % possible obs: 91 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Biso Wilson estimate: 34.08 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 23.7
Reflection shellResolution: 2.14→2.28 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 8.03 / Rsym value: 0.257 / % possible all: 80

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→8 Å / Cor.coef. Fo:Fc: 0.9415 / Cor.coef. Fo:Fc free: 0.8965 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1861 4.96 %RANDOM
Rwork0.1964 ---
obs0.1994 37531 85.85 %-
all-39701 --
Displacement parametersBiso mean: 37.97 Å2
Baniso -1Baniso -2Baniso -3
1--1.4485 Å20 Å20 Å2
2---1.5572 Å20 Å2
3---3.0057 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.12→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5875 0 58 111 6044
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016056HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.258231HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2046SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes137HARMONIC2
X-RAY DIFFRACTIONt_gen_planes915HARMONIC5
X-RAY DIFFRACTIONt_it6056HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
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_contact
LS refinement shellResolution: 2.12→2.18 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.3036 85 3.34 %
Rwork0.2356 2458 -
all0.2379 2543 -
obs--85.85 %

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