SAXSdb — 2dy1

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

Elongation factor G

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 GUANOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SI76_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–665； UniProt 1–658

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2dy1
Deposition date deposition_date	2006-09-04
Structure title title	Crystal structure of EF-G-2 from Thermus thermophilus
Keywords keywords	;Translocation, ELONGATION, GTP Complex, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, SIGNALING PROTEIN, TRANSLATION ;; SIGNALING PROTEIN, TRANSLATION
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2dy1__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2dy1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dy1__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.65 Å
Rg (electron density)	32.47 Å
Total Rg	32.73 Å
Atom count	5167
Residues	660
Excluded volume	92011 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dy1__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Elongation factor G
Molecular weight formula_weight	73232.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5765

MGTEGGAMIRTVALVGHAGSGKTTLTEALLYKTGAKERRGRVEEGTTTTDYTPEAKLHRTTVRTGVAPLLFRGHRVFLLDAPGYGDFVGEIRGALEAADAALVAVSAEAGVQVGTERAWTVAERLGLPRMVVVTKLDKGGDYYALLEDLRSTLGPILPIDLPLYEGGKWVGLIDVFHGKAYRYENGEEREAEVPPEERERVQRFRQEVLEAIVETDEGLLEKYLEGEEVTGEALEKAFHEAVRRGLLYPVALASGEREIGVLPLLELILEALPSPTERFGDGPPLAKVFKVQVDPFMGQVAYLRLYRGRLKPGDSLQSEAGQVRLPHLYVPMGKDLLEVEEAEAGFVLGVPKAEGLHRGMVLWQGEKPESEEVPFARLPDPNVPVALHPKGRTDEARLGEALRKLLEEDPSLKLERQEETGELLLWGHGELHLATAKERLQDYGVEVEFSVPKVPYRETIKKVAEGQGKYKKQTGGHGQYGDVWLRLEPASEYGFEWRITGGVIPSKYQEAIEEGIKEAAKKGVLAGFPVMGFKAIVYNGSYHEVDSSDLAFQIAASLAFKKVMAEAHPVLLEPIYRLKVLAPQERVGDVLSDLQARRGRILGMEQEGALSVVHAEVPLAEVLEYYKALPGLTGGAGAYTLEFSHYAEVPPHLAQRIVQERAQEG

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	598

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2dy1a1
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.3 — Translation proteins
Family Family family	b.43.3.1 — Elongation factors

Domain ID domain_id	d2dy1a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d2dy1a3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.1 — Translational machinery components

Domain ID domain_id	d2dy1a4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.11 — EF-G C-terminal domain-like
Family Family family	d.58.11.1 — EF-G/eEF-2 domains III and V

Domain ID domain_id	d2dy1a5
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.11 — EF-G C-terminal domain-like
Family Family family	d.58.11.1 — EF-G/eEF-2 domains III and V

Domain ID domain_id	d2dy1a6
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	2dy1A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2dy1A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	2dy1A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	870 — Elongation Factor G (Translational Gtpase), domain 3

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Unit-cell length a length_a	159.194 Å
Unit-cell length b length_b	56.129 Å
Unit-cell length c length_c	92.189 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.57 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	35.610 Å
R factor r_factor	0.1880
R_work r_work	0.1880
R_free r_free	0.2040

Crystal structure of EF-G-2 from Thermus thermophilus

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

Elongation factor G

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2dy1__assembly_1__model_1

2dy1__assembly_1__model_1 | I(q)

2dy1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of EF-G-2 from Thermus thermophilus

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

Elongation factor G

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2dy1__assembly_1__model_1

2dy1__assembly_1__model_1 | I(q)

2dy1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. Citations (1)