1ktv

Crystal Structure of Elongation Factor G Dimer Without Nucleotide

Method: X-RAY DIFFRACTION Dmax: 137.7 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

ELONGATION FACTOR G

Thermus thermophilus

UniProt P13551

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 1–691 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.6;293 K;PEG 8000, HEPES, Tris, Dithiothreitol, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.80 Å R-free 0.374
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–691 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.6;293 K;PEG 8000, HEPES, Tris, Dithiothreitol, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.80 Å R-free 0.374

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.

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EFG_THETH
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–691; UniProt 1–691 Author chain B; PDBConstruct 1–691; UniProt 1–691

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 1ktv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ktv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ktv
Deposition date deposition_date2002-01-17
Structure title titleCrystal Structure of Elongation Factor G Dimer Without Nucleotide
Keywords keywordsapo form, TRANSLATION; TRANSLATION
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier39.19
Radius of gyration Rg (electron density) rg_electron38.78
Forward intensity I(0) i0289251000.00
Molecular weight molecular_weight140770.0 kDa
Excluded volume excluded_volume177700 ų
Envelope volume envelope_volume242650 ų
Hydration-shell volume shell_volume53267 ų
Envelope diameter envelope_diameter145.4
Shell Rg shell_rg43.51
Envelope Rg envelope_rg38.19
Shape Rg shape_rg38.79
Total Rg total_rg39.06
Total atoms total_atoms9914
Residues n_residues1264
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax137.7
Rg (real space) rg_real39.14
Rg uncertainty (real space) rg_real_error1.16
I(0) (real space) i0_real2.8930e+08
I(0) uncertainty (real space) i0_real_error4.5480e+06
Rg (reciprocal space) rg_reciprocal39.17
I(0) (reciprocal space) i0_reciprocal289300000.0000
Solution quality estimate total_estimate0.8784
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary48.2
Skewness Skewness skewness0.282
Kurtosis Kurtosis kurtosis-0.353
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha24180000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.818; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.977

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1ktva1
Class classb — All beta proteins
Fold Fold foldb.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamilyb.43.3 — Translation proteins
Family Family familyb.43.3.1 — Elongation factors
Domain ID domain_idd1ktva2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd1ktva3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamilyd.14.1 — Ribosomal protein S5 domain 2-like
Family Family familyd.14.1.1 — Translational machinery components
Domain ID domain_idd1ktva4
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.11 — EF-G C-terminal domain-like
Family Family familyd.58.11.1 — EF-G/eEF-2 domains III and V
Domain ID domain_idd1ktvb1
Class classb — All beta proteins
Fold Fold foldb.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamilyb.43.3 — Translation proteins
Family Family familyb.43.3.1 — Elongation factors
Domain ID domain_idd1ktvb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd1ktvb3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamilyd.14.1 — Ribosomal protein S5 domain 2-like
Family Family familyd.14.1.1 — Translational machinery components
Domain ID domain_idd1ktvb4
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.11 — EF-G C-terminal domain-like
Family Family familyd.58.11.1 — EF-G/eEF-2 domains III and V

CATH v4.4 (10 domains)

Domain ID domain_id1ktvA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1ktvA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id1ktvA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily870 — Elongation Factor G (Translational Gtpase), domain 3
Domain ID domain_id1ktvA04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily10
Domain ID domain_id1ktvA05
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily240
Domain ID domain_id1ktvB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1ktvB02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id1ktvB03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily870 — Elongation Factor G (Translational Gtpase), domain 3
Domain ID domain_id1ktvB04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily10
Domain ID domain_id1ktvB05
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily240

8. Citations (1)

9. Files and Curves (10)