SAXSdb — 9hmp

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

tRNA threonylcarbamoyladenosine dehydratase 1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ADENOSINE MONOPHOSPHATE × 2 CHLORIDE ION × 2 SODIUM ION × 6 GLYCEROL × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ADENOSINE MONOPHOSPHATE × 2 CHLORIDE ION × 3 SODIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TCD1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–382； UniProt 50–429 Author chain B； PDBConstruct 3–382； UniProt 50–429 Author chain C； PDBConstruct 3–382； UniProt 50–429 Author chain D； PDBConstruct 3–382； UniProt 50–429

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	9hmp
Deposition date deposition_date	2024-12-09
Structure title title	X-ray structure of S. cerevisiae threonylcarbamoyladenosine dehydratase 1 (residues 50-429) in complex with AMP
Keywords keywords	tRNA, modification, threonylcarbamoyladenosine dehydratase, cyclic N6-threonylcarbamoyladenosine, ct6A, yeast, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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.

9hmp__assembly_1__model_1

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

Download this curve (.dat)

9hmp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9hmp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.35 Å
Rg (electron density)	30.83 Å
Total Rg	31.29 Å
Atom count	5847
Residues	724
Excluded volume	104780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9hmp__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9hmp__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Description description	tRNA threonylcarbamoyladenosine dehydratase 1
Molecular weight formula_weight	43527.9 kDa
EC 编号 ec_number	6.1.-.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11707

GSDHLFREQLARNYAFLGEEGMRKIKEQYIVIVGAGEVGSWVCTMLIRSGCQKIMIIDPENISIDSLNTHCCAVLSDIGKPKVQCLKEHLSKIAPWSEIKARAKAWTKENSHDLIFADGESPTFIVDCLDNLESKVDLLEYAHHNKIDVISSMGVATKSDPTRVSINDISMTEFDPISRCVRRKLRKRGIATGISVVFSNEMLDPRRDDILSPIDCEHRAINAVRDEALRHLPELGTMPGIFGLSIATWILTKVSGYPMKENEVKNRLKFYDSILETFQKQMARLNENKERSSLLGLEEVGYIVEEMFRGKSPISGYSTKLALTKWEANKEISLTNVVLMTKEEQEIHEKRILLDGEKLTAVYSEEVLDFIERLFKEEEYYS

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3

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Unit-cell length a length_a	259.440 Å
Unit-cell length b length_b	259.440 Å
Unit-cell length c length_c	236.110 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	48

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	4.000 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2569
R_work r_work	0.2546
R_free r_free	0.2992

X-ray structure of S. cerevisiae threonylcarbamoyladenosine dehydratase 1 (residues 50-429) in complex with AMP

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

tRNA threonylcarbamoyladenosine dehydratase 1

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

9hmp__assembly_1__model_1

9hmp__assembly_1__model_1 | I(q)

9hmp__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

X-ray structure of S. cerevisiae threonylcarbamoyladenosine dehydratase 1 (residues 50-429) in complex with AMP

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

tRNA threonylcarbamoyladenosine dehydratase 1

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

9hmp__assembly_1__model_1

9hmp__assembly_1__model_1 | I(q)

9hmp__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)