SAXSdb — 9var

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

dTDP-4-dehydrorhamnose 3,5-epimerase

Methanothermobacter thermautotrophicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 2 SODIUM ION × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 2 SODIUM ION × 1 SULFATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RMLC_METTH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–188； UniProt 1–185 Author chain B； PDBConstruct 4–188； UniProt 1–185 Author chain C； PDBConstruct 4–188； UniProt 1–185 Author chain D； PDBConstruct 4–188； UniProt 1–185

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	9var
Deposition date deposition_date	2025-06-04
Structure title title	Crystal structure of Cu-bound artificial metalloprotein incorporating a TP ligand
Keywords keywords	noncanonical amino acids, METAL BINDING PROTEIN; METAL 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.

9var__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9var__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9var__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.72 Å
Rg (electron density)	21.73 Å
Total Rg	22.61 Å
Atom count	3095
Residues	368
Excluded volume	54428 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9var__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9var__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 (5)

Entity 1 Entity 1 polymer

Description description	dTDP-4-dehydrorhamnose 3,5-epimerase
Molecular weight formula_weight	22118.7 kDa
EC 编号 ec_number	5.1.3.13
Mutation mutation	R79 mutation
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	6352

GSHMAEFRFIKTSLDGAIIIEPEVYTDERGYFMETFNEAIFQENGLEVRFVQDNESMSVRGVLRGLHFQREKPQGKLVRVIXGEIFDVAVDLRKNSDTYGEWTGVRLSDENRREFFIPEGFAHGFLALSDECIVNYKCTELYHPEYDSGIPWDDPDIGIDWPLEMVDDLIISEKDRNWKPLRENPVYL

Source Source

Source organism organism	Methanothermobacter thermautotrophicus
NCBI taxonomy ID ncbi_taxonomy_id	145262
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	167

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Unit-cell length a length_a	51.582 Å
Unit-cell length b length_b	72.741 Å
Unit-cell length c length_c	63.520 Å
Unit-cell angle α angle_alpha	90.05 °
Unit-cell angle β angle_beta	113.49 °
Unit-cell angle γ angle_gamma	89.89 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.862 Å
Low-resolution limit resolution_low	29.130 Å
R factor r_factor	0.2272
R_work r_work	0.2248
R_free r_free	0.2736

Crystal structure of Cu-bound artificial metalloprotein incorporating a TP ligand

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

dTDP-4-dehydrorhamnose 3,5-epimerase

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

9var__assembly_2__model_1

9var__assembly_2__model_1 | I(q)

9var__assembly_2__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 (5)

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 water

7. Citations (1)

Crystal structure of Cu-bound artificial metalloprotein incorporating a TP ligand

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

dTDP-4-dehydrorhamnose 3,5-epimerase

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

9var__assembly_2__model_1

9var__assembly_2__model_1 | I(q)

9var__assembly_2__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 (5)

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 water

7. Citations (1)