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3hk7

Crystal structure of uronate isomerase from Bacillus halodurans complexed with zinc and D-Arabinarate, monoclinic crystal form

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Uronate isomerase

Bacillus halodurans C-125

UniProt Q9KFI6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 7 D-arabinaric acid × 7 CARBONATE ION × 8 ZINC ION × 7 SODIUM ION × 3 CHLORIDE ION × 2 water × 7 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 8 D-arabinaric acid × 8 CARBONATE ION × 7 ZINC ION × 8 SODIUM ION × 4 CHLORIDE ION × 3 water × 8 Consistent with protein count
3 Protein homooligomer Homooligomer Protein 9 D-arabinaric acid × 9 CARBONATE ION × 8 ZINC ION × 9 SODIUM ION × 2 CHLORIDE ION × 3 water × 9 Consistent with protein count
4 Protein homooligomer Homooligomer Protein 7 D-arabinaric acid × 7 CARBONATE ION × 6 ZINC ION × 7 SODIUM ION × 2 CHLORIDE ION × 2 water × 7 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers
2pnk 2pnk 2pnk 2pnk 2pnk 2pnk 2q08 2q08 2q08 2q08 2q6e 2qee

28 assemblies; showing the first 12

Heteromeric or nucleic-acid complex

None

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 Author chain C； PDBConstruct 1–427； UniProt 1–427 Author chain D； PDBConstruct 1–427； UniProt 1–427 Author chain E； PDBConstruct 1–427； UniProt 1–427 Author chain F； PDBConstruct 1–427； UniProt 1–427 Author chain G； PDBConstruct 1–427； UniProt 1–427 Author chain H； PDBConstruct 1–427； UniProt 1–427 Author chain I； PDBConstruct 1–427； UniProt 1–427 Author chain J； PDBConstruct 1–427； UniProt 1–427 Author chain K； PDBConstruct 1–427； UniProt 1–427 Author chain L； 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_id3hk7
Deposition date deposition_date2009-05-22
Structure title titleCrystal structure of uronate isomerase from Bacillus halodurans complexed with zinc and D-Arabinarate, monoclinic crystal form
Keywords keywordsuronate isomerase, Mechanism of the reaction, D-Arabinarate, ISOMERASE; ISOMERASE
Experimental Method methodX-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.

3hk7__assembly_2__model_1

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

Download this curve (.dat)

3hk7__assembly_2__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3hk7__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）58.05 Å
Rg (electron density)57.95 Å
Total Rg57.87 Å
Atom count27371
Residues3304
Excluded volume485950 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3hk7__assembly_1__model_1 heptameric （7） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3hk7__assembly_2__model_1 octameric （8） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3hk7__assembly_3__model_1 nonameric （9） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3hk7__assembly_4__model_1 heptameric （7） 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)

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd3hk7a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.8 — Uronate isomerase-like
Domain ID domain_idd3hk7b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.8 — Uronate isomerase-like
Domain ID domain_idd3hk7c_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.8 — Uronate isomerase-like
Domain ID domain_idd3hk7d_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.8 — Uronate isomerase-like
Domain ID domain_idd3hk7e_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.8 — Uronate isomerase-like
Domain ID domain_idd3hk7f_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.8 — Uronate isomerase-like
Domain ID domain_idd3hk7g_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.8 — Uronate isomerase-like
Domain ID domain_idd3hk7h_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.8 — Uronate isomerase-like
Domain ID domain_idd3hk7i_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.8 — Uronate isomerase-like
Domain ID domain_idd3hk7j_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.8 — Uronate isomerase-like
Domain ID domain_idd3hk7k_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.8 — Uronate isomerase-like
Domain ID domain_idd3hk7l_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.8 — Uronate isomerase-like

CATH v4.4 (12 domains)

Domain ID domain_id3hk7A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology2020 — uronate isomerase, domain 2, chain A
Homologous superfamily homologous superfamily10 — uronate isomerase, domain 2, chain A
Domain ID domain_id3hk7B02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology2020 — uronate isomerase, domain 2, chain A
Homologous superfamily homologous superfamily10 — uronate isomerase, domain 2, chain A
Domain ID domain_id3hk7C02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology2020 — uronate isomerase, domain 2, chain A
Homologous superfamily homologous superfamily10 — uronate isomerase, domain 2, chain A
Domain ID domain_id3hk7D02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology2020 — uronate isomerase, domain 2, chain A
Homologous superfamily homologous superfamily10 — uronate isomerase, domain 2, chain A
Domain ID domain_id3hk7E02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology2020 — uronate isomerase, domain 2, chain A
Homologous superfamily homologous superfamily10 — uronate isomerase, domain 2, chain A
Domain ID domain_id3hk7F02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology2020 — uronate isomerase, domain 2, chain A
Homologous superfamily homologous superfamily10 — uronate isomerase, domain 2, chain A
Domain ID domain_id3hk7G02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology2020 — uronate isomerase, domain 2, chain A
Homologous superfamily homologous superfamily10 — uronate isomerase, domain 2, chain A
Domain ID domain_id3hk7H02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology2020 — uronate isomerase, domain 2, chain A
Homologous superfamily homologous superfamily10 — uronate isomerase, domain 2, chain A
Domain ID domain_id3hk7I02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology2020 — uronate isomerase, domain 2, chain A
Homologous superfamily homologous superfamily10 — uronate isomerase, domain 2, chain A
Domain ID domain_id3hk7J02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology2020 — uronate isomerase, domain 2, chain A
Homologous superfamily homologous superfamily10 — uronate isomerase, domain 2, chain A
Domain ID domain_id3hk7K02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology2020 — uronate isomerase, domain 2, chain A
Homologous superfamily homologous superfamily10 — uronate isomerase, domain 2, chain A
Domain ID domain_id3hk7L02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology2020 — uronate isomerase, domain 2, chain A
Homologous superfamily homologous superfamily10 — uronate isomerase, domain 2, chain A
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7. Citations (1)