6bgn

Crystal Structure of 4-Oxalocrotonate Tautomerase After Incubation with 5-Fluoro-2-hydroxy-2,4-pentadienoate

Method: X-RAY DIFFRACTION

▼

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

2-hydroxymuconate tautomerase

Pseudomonas putida

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	5-fluoranyl-2-oxidanylidene-pentanoic acid × 1 water × 1	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	5-fluoranyl-2-oxidanylidene-pentanoic acid × 1 GLYCEROL × 1 NITRATE ION × 1 water × 1	Consistent with protein count
11	Protein monomer	Monomer	Protein 1	5-fluoranyl-2-oxidanylidene-pentanoic acid × 1 GLYCEROL × 1 water × 1	Consistent with protein count
12	Protein monomer	Monomer	Protein 1	5-fluoranyl-2-oxidanylidene-pentanoic acid × 1 GLYCEROL × 1 water × 1	Consistent with protein count
13	Protein monomer	Monomer	Protein 1	5-fluoranyl-2-oxidanylidene-pentanoic acid × 1 GLYCEROL × 1 water × 1	Consistent with protein count
14	Protein monomer	Monomer	Protein 1	5-fluoranyl-2-oxidanylidene-pentanoic acid × 1 GLYCEROL × 1 water × 1	Consistent with protein count
15	Protein monomer	Monomer	Protein 1	5-fluoranyl-2-oxidanylidene-pentanoic acid × 1 GLYCEROL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	5-fluoranyl-2-oxidanylidene-pentanoic acid × 1 GLYCEROL × 3 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	5-fluoranyl-2-oxidanylidene-pentanoic acid × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	5-fluoranyl-2-oxidanylidene-pentanoic acid × 1 GLYCEROL × 2 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	5-fluoranyl-2-oxidanylidene-pentanoic acid × 1 GLYCEROL × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	5-fluoranyl-2-oxidanylidene-pentanoic acid × 1 GLYCEROL × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	5-fluoranyl-2-oxidanylidene-pentanoic acid × 1 GLYCEROL × 2 NITRATE ION × 1 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	5-fluoranyl-2-oxidanylidene-pentanoic acid × 1 GLYCEROL × 2 NITRATE ION × 1 water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	5-fluoranyl-2-oxidanylidene-pentanoic acid × 1 GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	4OT1_PSEPU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–60； UniProt 2–61 Author chain B； PDBConstruct 1–60； UniProt 2–61 Author chain C； PDBConstruct 1–60； UniProt 2–61 Author chain D； PDBConstruct 1–60； UniProt 2–61 Author chain E； PDBConstruct 1–60； UniProt 2–61 Author chain F； PDBConstruct 1–60； UniProt 2–61 Author chain G； PDBConstruct 1–60； UniProt 2–61 Author chain H； PDBConstruct 1–60； UniProt 2–61 Author chain I； PDBConstruct 1–60； UniProt 2–61 Author chain J； PDBConstruct 1–60； UniProt 2–61 Author chain K； PDBConstruct 1–60； UniProt 2–61 Author chain L； PDBConstruct 1–60； UniProt 2–61 Author chain M； PDBConstruct 1–60； UniProt 2–61 Author chain N； PDBConstruct 1–60； UniProt 2–61 Author chain O； PDBConstruct 1–60； UniProt 2–61

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6bgn
Deposition date deposition_date	2017-10-29
Structure title title	Crystal Structure of 4-Oxalocrotonate Tautomerase After Incubation with 5-Fluoro-2-hydroxy-2,4-pentadienoate
Keywords keywords	ISOMERASE; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6bgn__assembly_15__model_1

Assembly 15 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6bgn__assembly_15__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6bgn__assembly_15__model_1 | P(r) · Pending

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

Rg（Guinier）	15.07 Å
Rg (electron density)	14.02 Å
Total Rg	15.01 Å
Atom count	463
Residues	59
Excluded volume	8284 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6bgn__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6bgn__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6bgn__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6bgn__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6bgn__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`6bgn__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`6bgn__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`6bgn__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`6bgn__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`6bgn__assembly_10__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`6bgn__assembly_11__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`6bgn__assembly_12__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
13	1	`6bgn__assembly_13__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
14	1	`6bgn__assembly_14__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
15	1	`6bgn__assembly_15__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	2-hydroxymuconate tautomerase
Molecular weight formula_weight	6507.4 kDa
EC 编号 ec_number	5.3.2.6
Source method src_method	man
Copy count entity_count	15

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O
Atom count atom_count	7904

PIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASKV

Source Source

Source organism organism	Pseudomonas putida
Common name common_name	Arthrobacter siderocapsulatus
NCBI taxonomy ID ncbi_taxonomy_id	303
Host organism host_organism	Escherichia coli K-12

Entity 2 Entity 2 non-polymer

Description description	5-fluoranyl-2-oxidanylidene-pentanoic acid
Molecular weight formula_weight	134.1 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 4 Entity 4 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	637

▼

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (15 domains)

Domain ID domain_id	d6bgna_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d6bgnb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d6bgnc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d6bgnd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d6bgne_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d6bgnf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d6bgng_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d6bgnh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d6bgni_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d6bgnj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d6bgnk_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d6bgnl_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d6bgnm_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d6bgnn_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d6bgno_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

CATH v4.4 (15 domains)

Domain ID domain_id	6bgnA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6bgnB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6bgnC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6bgnD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6bgnE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6bgnF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6bgnG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6bgnH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6bgnI00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6bgnJ00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6bgnK00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6bgnL00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6bgnM00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6bgnN00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6bgnO00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

▶

Unit-cell length a length_a	87.413 Å
Unit-cell length b length_b	88.011 Å
Unit-cell length c length_c	112.674 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.26 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	60

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

Resolution resolution	1.510 Å
Low-resolution limit resolution_low	43.290 Å
R factor r_factor	0.1183
R_work r_work	0.1156
R_free r_free	0.1694

Crystal Structure of 4-Oxalocrotonate Tautomerase After Incubation with 5-Fluoro-2-hydroxy-2,4-pentadienoate

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

2-hydroxymuconate tautomerase

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

6bgn__assembly_15__model_1

6bgn__assembly_15__model_1 | I(q)

6bgn__assembly_15__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

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (15 domains)

CATH v4.4 (15 domains)

7. Citations (1)

Crystal Structure of 4-Oxalocrotonate Tautomerase After Incubation with 5-Fluoro-2-hydroxy-2,4-pentadienoate

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

2-hydroxymuconate tautomerase

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

6bgn__assembly_15__model_1

6bgn__assembly_15__model_1 | I(q)

6bgn__assembly_15__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

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (15 domains)

CATH v4.4 (15 domains)

7. Citations (1)