SAXSdb — 9xs8

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

Cupin type-2 domain-containing protein

Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	1-methyl-4-(1-methylethyl)benzene × 1 RUTHENIUM ION × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9X1H0_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–118； UniProt 1–114 Author chain B； PDBConstruct 5–118； UniProt 1–114

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	9xs8
Deposition date deposition_date	2025-11-20
Last revision last_revision	2026-04-29
Structure title title	Crystal structure of a cupin protein (tm1459, H52A/H54A/H92A/C106E mutant) in ruthenium(p-cymene) bound form
Keywords keywords	Artificial metalloenzymes, Biocatalysis, Ruthenium(p-cymene), 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.

9xs8__assembly_1__model_1

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

Download this curve (.dat)

9xs8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9xs8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.69 Å
Rg (electron density)	17.20 Å
Total Rg	18.21 Å
Atom count	3650
Residues	231
Excluded volume	33083 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9xs8__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 (5)

Entity 1 Entity 1 polymer

Description description	Cupin type-2 domain-containing protein
Molecular weight formula_weight	13252.1 kDa
Mutation mutation	H52A/H54A/H92A/C106E
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3875

GPSGMILKRAYDVTPQKISTDKVRGVRKRVLIGLKDAPNFVMRLFTVEPGGLIDRASAPWEHEIFVLKGKLTVLKEQGEETVEEGFYIFVEPNEIAGFRNDTDSEVEFLELIPKEGGE

Source Source

Source organism organism	Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	1-methyl-4-(1-methylethyl)benzene
Molecular weight formula_weight	134.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	RUTHENIUM ION
Molecular weight formula_weight	101.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 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	201

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Unit-cell length a length_a	50.810 Å
Unit-cell length b length_b	57.630 Å
Unit-cell length c length_c	74.500 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.265 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1487
R_work r_work	0.1474
R_free r_free	0.1981

Crystal structure of a cupin protein (tm1459, H52A/H54A/H92A/C106E mutant) in ruthenium(p-cymene) bound form

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

Cupin type-2 domain-containing protein

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

9xs8__assembly_1__model_1

9xs8__assembly_1__model_1 | I(q)

9xs8__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 (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 a cupin protein (tm1459, H52A/H54A/H92A/C106E mutant) in ruthenium(p-cymene) bound form

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

Cupin type-2 domain-containing protein

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

9xs8__assembly_1__model_1

9xs8__assembly_1__model_1 | I(q)

9xs8__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 (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)