3sbf

Crystal structure of the mutant P311A of enolase superfamily member from VIBRIONALES BACTERIUM complexed with Mg and D-Arabinonate

Method: X-RAY DIFFRACTION

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

mandelate racemase / muconate lactonizing enzyme

Vibrionales bacterium SWAT-3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 D-arabinonic acid × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 3 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 D-arabinonic acid × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 D-arabinonic acid × 2 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 3 D-arabinonic acid × 2 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 6 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 D-arabinonic acid × 4 water × 4	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 4 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 D-arabinonic acid × 4 water × 4	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 8	MAGNESIUM ION × 10 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 4 D-arabinonic acid × 8 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A5KUH4_9GAMM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–401； UniProt 2–399 Author chain B； PDBConstruct 4–401； UniProt 2–399 Author chain C； PDBConstruct 4–401； UniProt 2–399 Author chain D； PDBConstruct 4–401； UniProt 2–399

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	3sbf
Deposition date deposition_date	2011-06-04
Structure title title	Crystal structure of the mutant P311A of enolase superfamily member from VIBRIONALES BACTERIUM complexed with Mg and D-Arabinonate
Keywords keywords	enolase fold, acid sugar dehydratase, D-Araninonate, 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.

3sbf__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3sbf__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3sbf__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	30.25 Å
Rg (electron density)	29.47 Å
Total Rg	30.04 Å
Atom count	6380
Residues	794
Excluded volume	112920 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3sbf__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3sbf__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3sbf__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3sbf__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3sbf__assembly_5__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3sbf__assembly_6__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3sbf__assembly_7__model_1`	octameric （8）	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	mandelate racemase / muconate lactonizing enzyme
Molecular weight formula_weight	45378.4 kDa
Mutation mutation	P311A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	14132

MSLKETIISDIHCIITKPDRHNLITVVVETNEGVTGFGCATFQQRPLAVKTMVDEYLKPILIGKNANNIEDLWQMMMVNAYWRNGPVINNAISGVDMALWDIKAKLAGMPLHQLFGGKSRDAIPVYTHATSDTMEGIYDLVEGFLEKGYKHIRCQLGFYGGVPTDLHTTQNPTEGSYYDQDQYMDNTLTMFKSLREKYGNQFHILHDVHERLFPNQAIQFAKEVEQYKPYFIEDILPPNQTEWLDNIRSQSSVSLGLGELFNNPEEWKSLIANRRIDFIRCHVSQIGGITPALKLGHLCQNFGVRIAWHCAPDMTPIGAAVNTHLNVHLHNAAIQEHVEYNGNTHKVFPNAAEPINGYLYASEIAGIGVEIDREAAAEFPVMYRPHEWTQSRLPDGAIHTP

Source Source

Source organism organism	Vibrionales bacterium SWAT-3
NCBI taxonomy ID ncbi_taxonomy_id	391574
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	D-arabinonic acid
Molecular weight formula_weight	166.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1397

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6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d3sbfa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
Family Family family	d.54.1.0 — automated matches

Domain ID domain_id	d3sbfa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.11 — Enolase C-terminal domain-like
Family Family family	c.1.11.2 — D-glucarate dehydratase-like

Domain ID domain_id	d3sbfb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
Family Family family	d.54.1.0 — automated matches

Domain ID domain_id	d3sbfb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.11 — Enolase C-terminal domain-like
Family Family family	c.1.11.2 — D-glucarate dehydratase-like

Domain ID domain_id	d3sbfc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
Family Family family	d.54.1.0 — automated matches

Domain ID domain_id	d3sbfc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.11 — Enolase C-terminal domain-like
Family Family family	c.1.11.2 — D-glucarate dehydratase-like

Domain ID domain_id	d3sbfd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
Family Family family	d.54.1.0 — automated matches

Domain ID domain_id	d3sbfd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.11 — Enolase C-terminal domain-like
Family Family family	c.1.11.2 — D-glucarate dehydratase-like

Domain ID domain_id	d3sbfd3
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

CATH v4.4 (8 domains)

Domain ID domain_id	3sbfA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

Domain ID domain_id	3sbfA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	120 — Enolase-like C-terminal domain

Domain ID domain_id	3sbfB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

Domain ID domain_id	3sbfB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	120 — Enolase-like C-terminal domain

Domain ID domain_id	3sbfC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

Domain ID domain_id	3sbfC02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	120 — Enolase-like C-terminal domain

Domain ID domain_id	3sbfD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

Domain ID domain_id	3sbfD02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	120 — Enolase-like C-terminal domain

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Unit-cell length a length_a	163.372 Å
Unit-cell length b length_b	163.372 Å
Unit-cell length c length_c	110.412 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	32

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	46.794 Å
R factor r_factor	0.1811
R_work r_work	0.1797
R_free r_free	0.2065

Crystal structure of the mutant P311A of enolase superfamily member from VIBRIONALES BACTERIUM complexed with Mg and D-Arabinonate

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

mandelate racemase / muconate lactonizing enzyme

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

3sbf__assembly_3__model_1

3sbf__assembly_3__model_1 | I(q)

3sbf__assembly_3__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) 17 domains

SCOP 2.08 (9 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of the mutant P311A of enolase superfamily member from VIBRIONALES BACTERIUM complexed with Mg and D-Arabinonate

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

mandelate racemase / muconate lactonizing enzyme

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

3sbf__assembly_3__model_1

3sbf__assembly_3__model_1 | I(q)

3sbf__assembly_3__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) 17 domains

SCOP 2.08 (9 domains)

CATH v4.4 (8 domains)

7. Citations (1)