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8fr3

E. coli EF-Tu in complex with KKL-55

Method: X-RAY DIFFRACTION Dmax: 90.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Elongation factor Tu

Escherichia coli K-12

UniProt E2QFJ4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–394 Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 Y7C 3-chloro-N-(1-propyl-1H-tetrazol-5-yl)benzamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；30-35% polyethylene glycol monomethyl ether 5,000 (PEG 5K MME), 0.2 M (NH4)2(SO4), 0.1 M MES pH 6.5 Resolution 2.23 Å R-free 0.275
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–394 Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；30-35% polyethylene glycol monomethyl ether 5,000 (PEG 5K MME), 0.2 M (NH4)2(SO4), 0.1 M MES pH 6.5 Resolution 2.23 Å R-free 0.275

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8FR3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WD2 Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-A) Deposited 2020-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric
Chain 8 2–394（393 aa）
Not recorded FME N-FORMYLMETHIONINE × 1 PHE PHENYLALANINE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6WD3 Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-B1) Deposited 2020-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric
Chain 8 2–394（393 aa）
Not recorded FME N-FORMYLMETHIONINE × 1 PHE PHENYLALANINE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6WD4 Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-B2) Deposited 2020-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric
Chain 8 2–394（393 aa）
Not recorded FME N-FORMYLMETHIONINE × 1 PHE PHENYLALANINE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6WD5 Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-C1) Deposited 2020-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric
Chain 8 2–394（393 aa）
Not recorded FME N-FORMYLMETHIONINE × 1 PHE PHENYLALANINE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6WD6 Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-C2) Deposited 2020-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric
Chain 8 2–394（393 aa）
Not recorded FME N-FORMYLMETHIONINE × 1 PHE PHENYLALANINE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6WD7 Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-D) Deposited 2020-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric
Chain 8 2–394（393 aa）
Not recorded FME N-FORMYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6WD8 Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure III-A) Deposited 2020-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric
Chain 8 2–394（393 aa）
Not recorded FME N-FORMYLMETHIONINE × 1 PHE PHENYLALANINE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6WD9 Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure III-B) Deposited 2020-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric
Chain 8 2–394（393 aa）
Not recorded FME N-FORMYLMETHIONINE × 1 PHE PHENYLALANINE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6WDA Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure III-C) Deposited 2020-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric
Chain 8 2–394（393 aa）
Not recorded FME N-FORMYLMETHIONINE × 1 PHE PHENYLALANINE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name E2QFJ4_ECOLX
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–394； UniProt 1–394 Author chain B； PDBConstruct 1–394； UniProt 1–394

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8fr3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8fr3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8fr3
Deposition date deposition_date2023-01-06
Structure title titleE. coli EF-Tu in complex with KKL-55
Keywords keywordsEF-Tu, translation, antibiotic; TRANSLATION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.54 Å
Radius of gyration Rg (electron density) rg_electron28.75 Å
Forward intensity I(0) i0119602000.00
Molecular weight molecular_weight85515.0 kDa
Excluded volume excluded_volume106910 ų
Envelope volume envelope_volume135800 ų
Hydration-shell volume shell_volume39226 ų
Envelope diameter envelope_diameter93.2 Å
Shell Rg shell_rg36.26 Å
Envelope Rg envelope_rg28.05 Å
Shape Rg shape_rg28.72 Å
Total Rg total_rg29.56 Å
Total atoms total_atoms6006
Residues n_residues770
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax90.2 Å
Rg (real space) rg_real29.37 Å
Rg uncertainty (real space) rg_real_error0.57 Å
I(0) (real space) i0_real1.1960e+08
I(0) uncertainty (real space) i0_real_error1.6720e+06
Rg (reciprocal space) rg_reciprocal29.44 Å
I(0) (reciprocal space) i0_reciprocal119600000.0000
Solution quality estimate total_estimate0.9065
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.8 Å
Skewness Skewness skewness0.094
Kurtosis Kurtosis kurtosis-0.515
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha41200000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.980
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)