SAXSdb — 3hk8

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

Uronate isomerase

Bacillus halodurans C-125

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	D-arabinohydroxamic acid × 6 CARBONATE ION × 6 ZINC ION × 12 CHLORIDE ION × 6 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	D-arabinohydroxamic acid × 6 CARBONATE ION × 6 ZINC ION × 12 CHLORIDE ION × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9KFI6_BACHD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–427； UniProt 1–427 Author chain B； PDBConstruct 1–427； UniProt 1–427

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	3hk8
Deposition date deposition_date	2009-05-22
Structure title title	Crystal structure of uronate isomerase from Bacillus halodurans complexed with zinc and D-Arabinohydroxamate
Keywords keywords	uronate isomerase, D-Arabinohydroxamate, Mechanism of the reaction, ISOMERASE; ISOMERASE
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.

3hk8__assembly_1__model_1

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

Download this curve (.dat)

3hk8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3hk8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.98 Å
Rg (electron density)	41.35 Å
Total Rg	41.63 Å
Atom count	20338
Residues	2454
Excluded volume	361050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3hk8__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3hk8__assembly_2__model_1`	hexameric （6）	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	Uronate isomerase
Molecular weight formula_weight	50006.9 kDa
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	7094

MSINSREVLAEKVKNAVNNQPVTDMHTHLFSPNFGEILLWDIDELLTYHYLVAEVMRWTDVSIEAFWAMSKREQADLIWEELFIKRSPVSEACRGVLTCLQGLGLDPATRDLQVYREYFAKKTSEEQVDTVLQLANVSDVVMTNDPFDDNERISWLEGKQPDSRFHAALRLDPLLNEYEQTKHRLRDWGYKVNDEWNEGSIQEVKRFLTDWIERMDPVYMAVSLPPTFSFPEESNRGRIIRDCLLPVAEKHNIPFAMMIGVKKRVHPALGDAGDFVGKASMDGVEHLLREYPNNKFLVTMLSRENQHELVVLARKFSNLMIFGCWWFMNNPEIINEMTRMRMEMLGTSFIPQHSDARVLEQLIYKWHHSKSIIAEVLIDKYDDILQAGWEVTEEEIKRDVADLFSRNFWRFVGRNDHVTSVKVEQQT

Source Source

Source organism organism	Bacillus halodurans C-125
NCBI taxonomy ID ncbi_taxonomy_id	272558
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	D-arabinohydroxamic acid
Molecular weight formula_weight	195.1 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CARBONATE ION
Molecular weight formula_weight	60.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	312

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3hk8a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.8 — Uronate isomerase-like

Domain ID domain_id	d3hk8b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.8 — Uronate isomerase-like

CATH v4.4 (2 domains)

Domain ID domain_id	3hk8A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	2020 — uronate isomerase, domain 2, chain A
Homologous superfamily homologous superfamily	10 — uronate isomerase, domain 2, chain A

Domain ID domain_id	3hk8B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	2020 — uronate isomerase, domain 2, chain A
Homologous superfamily homologous superfamily	10 — uronate isomerase, domain 2, chain A

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Unit-cell length a length_a	149.305 Å
Unit-cell length b length_b	149.305 Å
Unit-cell length c length_c	254.018 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	36

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	24.930 Å
R factor r_factor	0.2050
R_work r_work	0.2040
R_free r_free	0.2260

Crystal structure of uronate isomerase from Bacillus halodurans complexed with zinc and D-Arabinohydroxamate

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

Uronate isomerase

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

3hk8__assembly_1__model_1

3hk8__assembly_1__model_1 | I(q)

3hk8__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

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of uronate isomerase from Bacillus halodurans complexed with zinc and D-Arabinohydroxamate

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

Uronate isomerase

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

3hk8__assembly_1__model_1

3hk8__assembly_1__model_1 | I(q)

3hk8__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

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)