SAXSdb — 4x33

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

Diphthamide biosynthesis protein 3

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Protein ATS1 × 1 （P31386） FE (III) ION × 1 CHLORIDE ION × 8 1,2-DIMETHOXYETHANE × 1 MAGNESIUM ION × 1 water × 2	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 1–57； UniProt 1–57

Protein ATS1

Saccharomyces cerevisiae

UniProt P31386

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Diphthamide biosynthesis protein 3 × 1 （Q3E840） FE (III) ION × 1 CHLORIDE ION × 8 1,2-DIMETHOXYETHANE × 1 MAGNESIUM ION × 1 water × 2	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–333； UniProt 1–333

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	4x33
Deposition date deposition_date	2014-11-27
Structure title title	Structure of the Elongator cofactor complex Kti11/Kti13 at 1.45A
Keywords keywords	Electron transfer, tRNA modification, Complex, electron transport; ELECTRON TRANSPORT
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.

4x33__assembly_1__model_1

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

Download this curve (.dat)

4x33__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4x33__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.36 Å
Rg (electron density)	20.25 Å
Total Rg	21.12 Å
Atom count	5854
Residues	384
Excluded volume	52860 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4x33__assembly_1__model_1`	dimeric （2）	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 (7)

Entity 1 Entity 1 polymer

Description description	Diphthamide biosynthesis protein 3
Molecular weight formula_weight	7458.4 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	7034

MSTYDEIEIEDMTFEPENQMFTYPCPCGDRFQIYLDDMFEGEKVAVCPSCSLMIDVVHHHHHH

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Protein ATS1
Molecular weight formula_weight	36522.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSCVYAFGSNGQRQLGLGHDEDMDTPQRSVPGDDGAIVRKIACGGNHSVMLTNDGNLVGCGDNRRGELDSAQALRQVHDWRPVEVPAPVVDVACGWDTTVIVDADGRVWQRGGGCYEFTQQHVPLNSNDERIAVYGCFQNFVVVQGTRVYGWGSNTKCQLQEPKSRSLKEPVLVYDTGSVAVDYVAMGKDFMVIVDEGGRIVHASGRLPTGFELKQQQKRHNLVVLCMWTSIHLWNARLNTVESFGRGTHSQLFPQERLDFPIVGVATGSEHGILTTANQEGKSHCYNVYCWGWGEHGNCGPQKGSQPGLQLVGQYSGKPRVFGGCATTWIVL

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	1,2-DIMETHOXYETHANE
Molecular weight formula_weight	90.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	549

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4x33A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	660 — Microbial ribonuclease fold
Homologous superfamily homologous superfamily	10 — DPH Zinc finger

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Unit-cell length a length_a	49.790 Å
Unit-cell length b length_b	89.009 Å
Unit-cell length c length_c	163.530 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	21.230 Å
R factor r_factor	0.1511
R_work r_work	0.1497
R_free r_free	0.1762

Structure of the Elongator cofactor complex Kti11/Kti13 at 1.45A

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

Diphthamide biosynthesis protein 3

State in the Current Structure

Other States of the Same Protein in the Database

Protein ATS1

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

4x33__assembly_1__model_1

4x33__assembly_1__model_1 | I(q)

4x33__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Structure of the Elongator cofactor complex Kti11/Kti13 at 1.45A

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

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

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

4x33__assembly_1__model_1

4x33__assembly_1__model_1 | I(q)

4x33__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)