2dw6

Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate

Method: X-RAY DIFFRACTION

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

Bll6730 protein

Bradyrhizobium japonicum

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 D(-)-TARTARIC ACID × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 D(-)-TARTARIC ACID × 1 L(+)-TARTARIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q89FH0_BRAJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–389； UniProt 1–389 Author chain B； PDBConstruct 1–389； UniProt 1–389 Author chain C； PDBConstruct 1–389； UniProt 1–389 Author chain D； PDBConstruct 1–389； UniProt 1–389

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	2dw6
Deposition date deposition_date	2006-08-07
Structure title title	Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate
Keywords keywords	D-Tartrate Dehydratase, Enolase superfamily, D-tartrate, L-tartrate, LYASE; LYASE
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.

2dw6__assembly_1__model_1

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

Download this curve (.dat)

2dw6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dw6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.57 Å
Rg (electron density)	26.66 Å
Total Rg	27.57 Å
Atom count	6058
Residues	776
Excluded volume	107440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dw6__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2dw6__assembly_2__model_1`	dimeric （2）	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	Bll6730 protein
Molecular weight formula_weight	43053.0 kDa
EC 编号 ec_number	4.2.1.81
Mutation mutation	K184A
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	12582

MSVRIVDVREITKPISSPIRNAYIDFTKMTTSLVAVVTDVVREGKRVVGYGFNSNGRYGQGGLIRERFASRILEADPKKLLNEAGDNLDPDKVWAAMMINEKPGGHGERSVAVGTIDMAVWDAVAKIAGKPLFRLLAERHGVKANPRVFVYAAGGYYYPGKGLSMLRGEMRGYLDRGYNVVKMAIGGAPIEEDRMRIEAVLEEIGKDAQLAVDANGRFNLETGIAYAKMLRDYPLFWYEEVGDPLDYALQAALAEFYPGPMATGENLFSHQDARNLLRYGGMRPDRDWLQFDCALSYGLCEYQRTLEVLKTHGWSPSRCIPHGGHQMSLNIAAGLGLGGNESYPDLFQPYGGFPDGVRVENGHITMPDLPGIGFEGKSDLYKEMKALAE

Source Source

Source organism organism	Bradyrhizobium japonicum
NCBI taxonomy ID ncbi_taxonomy_id	375
Host organism host_organism	Escherichia coli BL21(DE3)

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	4

Entity 3 Entity 3 non-polymer

Description description	D(-)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	L(+)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	466

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2dw6a1
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	d2dw6a2
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	d2dw6b1
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	d2dw6b2
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	d2dw6c1
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	d2dw6c2
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	d2dw6d1
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	d2dw6d2
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

CATH v4.4 (8 domains)

Domain ID domain_id	2dw6A01
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	2dw6A02
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	2dw6B01
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	2dw6B02
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	2dw6C01
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	2dw6C02
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	2dw6D01
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	2dw6D02
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	150.997 Å
Unit-cell length b length_b	150.997 Å
Unit-cell length c length_c	444.101 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	48

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2110
R_work r_work	0.2090
R_free r_free	0.2320

Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate

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

Bll6730 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

2dw6__assembly_1__model_1

2dw6__assembly_1__model_1 | I(q)

2dw6__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 (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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate

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

Bll6730 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

2dw6__assembly_1__model_1

2dw6__assembly_1__model_1 | I(q)

2dw6__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 (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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)