2pnk

CRYSTAL STRUCTURE OF AN URONATE ISOMERASE (BH0493) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION

Method: X-RAY DIFFRACTION

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

BH0493 protein

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 3	SODIUM ION × 1 CHLORIDE ION × 1 FORMIC ACID × 3 GLYCEROL × 5 UNKNOWN LIGAND × 1 PHOSPHATE ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	CHLORIDE ION × 1 FORMIC ACID × 4 GLYCEROL × 4 PHOSPHATE ION × 2 ACETATE ION × 1 water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	SODIUM ION × 1 CHLORIDE ION × 4 FORMIC ACID × 3 GLYCEROL × 7 UNKNOWN LIGAND × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 ACETATE ION × 1 water × 3	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 3	SODIUM ION × 1 CHLORIDE ION × 2 FORMIC ACID × 4 GLYCEROL × 8 UNKNOWN LIGAND × 1 PHOSPHATE ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 3 ACETATE ION × 1 water × 3	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 6	SODIUM ION × 2 CHLORIDE ION × 3 FORMIC ACID × 7 GLYCEROL × 13 UNKNOWN LIGAND × 2 PHOSPHATE ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 4 ACETATE ION × 1 water × 6	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 6	SODIUM ION × 1 CHLORIDE ION × 5 FORMIC ACID × 7 GLYCEROL × 11 UNKNOWN LIGAND × 1 PHOSPHATE ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 ACETATE ION × 2 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 2–428； UniProt 1–427 Author chain B； PDBConstruct 2–428； UniProt 1–427 Author chain C； PDBConstruct 2–428； UniProt 1–427 Author chain D； PDBConstruct 2–428； UniProt 1–427 Author chain E； PDBConstruct 2–428； UniProt 1–427 Author chain F； PDBConstruct 2–428； UniProt 1–427 Author chain G； PDBConstruct 2–428； UniProt 1–427 Author chain H； PDBConstruct 2–428； UniProt 1–427 Author chain I； PDBConstruct 2–428； UniProt 1–427 Author chain J； PDBConstruct 2–428； UniProt 1–427 Author chain K； PDBConstruct 2–428； UniProt 1–427 Author chain L； PDBConstruct 2–428； 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	2pnk
Deposition date deposition_date	2007-04-24
Structure title title	CRYSTAL STRUCTURE OF AN URONATE ISOMERASE (BH0493) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION
Keywords keywords	URONATE ISOMERASE, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, 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.

2pnk__assembly_1__model_1

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

Download this curve (.dat)

2pnk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2pnk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.68 Å
Rg (electron density)	31.74 Å
Total Rg	32.05 Å
Atom count	10448
Residues	1216
Excluded volume	186180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2pnk__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2pnk__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2pnk__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2pnk__assembly_4__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2pnk__assembly_5__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2pnk__assembly_6__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 (10)

Entity 1 Entity 1 polymer

Description description	BH0493 protein
Molecular weight formula_weight	50861.1 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	45764

GMSINSREVLAEKVKNAVNNQPVTDMHTHLFSPNFGEILLWDIDELLTYHYLVAEVMRWTDVSIEAFWAMSKREQADLIWEELFIKRSPVSEACRGVLTCLQGLGLDPATRDLQVYREYFAKKTSEEQVDTVLQLANVSDVVMTNDPFDDNERISWLEGKQPDSRFHAALRLDPLLNEYEQTKHRLRDWGYKVNDEWNEGSIQEVKRFLTDWIERMDPVYMAVSLPPTFSFPEESNRGRIIRDCLLPVAEKHNIPFAMMIGVKKRVHPALGDAGDFVGKASMDGVEHLLREYPNNKFLVTMLSRENQHELVVLARKFSNLMIFGCWWFMNNPEIINEMTRMRMEMLGTSFIPQHSDARVLEQLIYKWHHSKSIIAEVLIDKYDDILQAGWEVTEEEIKRDVADLFSRNFWRFVGRNDHVTSVKVEQQT

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	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	3

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	8

Entity 4 Entity 4 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	14

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	24

Entity 6 Entity 6 non-polymer

Description description	UNKNOWN LIGAND
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 9 Entity 9 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3732

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6. Fold Classification (SCOP + CATH) 27 domains

SCOP 2.08 (15 domains)

Domain ID domain_id	d2pnka1
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	d2pnka2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2pnkb_
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	d2pnkc_
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	d2pnkd1
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	d2pnkd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2pnke_
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	d2pnkf_
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	d2pnkg_
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	d2pnkh_
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	d2pnki_
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	d2pnkj_
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	d2pnkk2
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	d2pnkk3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2pnkl_
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 (12 domains)

Domain ID domain_id	2pnkA02
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	2pnkB02
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	2pnkC02
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	2pnkD02
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	2pnkE02
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	2pnkF02
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	2pnkG02
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	2pnkH02
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	2pnkI02
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	2pnkJ02
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	2pnkK02
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	2pnkL02
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	273.720 Å
Unit-cell length b length_b	158.560 Å
Unit-cell length c length_c	181.240 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	48.564 Å
R factor r_factor	0.1490
R_work r_work	0.1480
R_free r_free	0.1780

CRYSTAL STRUCTURE OF AN URONATE ISOMERASE (BH0493) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION

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

BH0493 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

2pnk__assembly_1__model_1

2pnk__assembly_1__model_1 | I(q)

2pnk__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 (10)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 27 domains

SCOP 2.08 (15 domains)

CATH v4.4 (12 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF AN URONATE ISOMERASE (BH0493) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION

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

BH0493 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

2pnk__assembly_1__model_1

2pnk__assembly_1__model_1 | I(q)

2pnk__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 (10)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 27 domains

SCOP 2.08 (15 domains)

CATH v4.4 (12 domains)

7. Citations (1)