SAXSdb — 4d4o

▼

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

PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 6	FE (III) ION × 4 SULFATE ION × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATS1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–335； UniProt 1–333 Author chain B； PDBConstruct 3–335； UniProt 1–333 Author chain C； PDBConstruct 3–335； UniProt 1–333

PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3

Saccharomyces cerevisiae

UniProt Q3E840

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 6	FE (III) ION × 4 SULFATE ION × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPH3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 346–427； UniProt 1–82 Author chain B； PDBConstruct 346–427； UniProt 1–82 Author chain C； PDBConstruct 346–427； UniProt 1–82

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4d4o
Deposition date deposition_date	2014-10-30
Structure title title	Crystal Structure of the Kti11 Kti13 heterodimer Spacegroup P64
Keywords keywords	TRANSLATION, TRNA MODIFICATION, KTI11, KTI13, ELONGATOR, DIPHTHAMIDE MODIFICATION; TRANSLATION
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4d4o__assembly_1__model_1

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

Download this curve (.dat)

4d4o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4d4o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.66 Å
Rg (electron density)	38.34 Å
Total Rg	38.61 Å
Atom count	12692
Residues	1640
Excluded volume	222290 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4d4o__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3
Molecular weight formula_weight	46698.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6346

GAMSCVYAFGSNGQRQLGLGHDEDMDTPQRSVPGDDGAIVRKIACGGNHSVMLTNDGNLVGCGDNRRGELDSAQALRQVHDWRPVEVPAPVVDVACGWDTTVIVDADGRVWQRGGGCYEFTQQHVPLNSNDERIAVYGCFQNFVVVQGTRVYGWGSNTKCQLQEPKSRSLKEPVLVYDTGSVAVDYVAMGKDFMVIVDEGGRIVHASGRLPTGFELKQQQKRHNLVVLCMWTSIHLWNARLNTVESFGRGTHSQLFPQERLDFPIVGVATGSEHGILTTANQEGKSHCYNVYCWGWGEHGNCGPQKGSQPGLQLVGQYSGKPRVFGGCATTWIVLGSGSGSGSGSMSTYDEIEIEDMTFEPENQMFTYPCPCGDRFQIYLDDMFEGEKVAVCPSCSLMIDVVFDKEDLAEYYEEAGIHPPEPIAAAA

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;BAKER'S YEAST ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

▼

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4d4oc_
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.17 — CSL zinc finger
Family Family family	g.41.17.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	4d4oA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	660 — Microbial ribonuclease fold
Homologous superfamily homologous superfamily	10 — DPH Zinc finger

Domain ID domain_id	4d4oC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	660 — Microbial ribonuclease fold
Homologous superfamily homologous superfamily	10 — DPH Zinc finger

▶

Unit-cell length a length_a	151.270 Å
Unit-cell length b length_b	151.270 Å
Unit-cell length c length_c	107.140 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 64
Space-group number int_tables_number	172
Crystal system crystal_system	—

Resolution resolution	2.897 Å
Low-resolution limit resolution_low	75.635 Å
R factor r_factor	0.1991
R_work r_work	0.1980
R_free r_free	0.2188

Crystal Structure of the Kti11 Kti13 heterodimer Spacegroup P64

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

PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3

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

4d4o__assembly_1__model_1

4d4o__assembly_1__model_1 | I(q)

4d4o__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of the Kti11 Kti13 heterodimer Spacegroup P64

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

PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3

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

4d4o__assembly_1__model_1

4d4o__assembly_1__model_1 | I(q)

4d4o__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)