7c0c

Crystal structure of Azospirillum brasilense L-2-keto-3-deoxyarabonate dehydratase (apo form)

Method: X-RAY DIFFRACTION

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

L-2-keto-3-deoxyarabonate dehydratase

Azospirillum brasilense

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KDADA_AZOBR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–320； UniProt 2–309 Author chain B； PDBConstruct 13–320； UniProt 2–309 Author chain C； PDBConstruct 13–320； UniProt 2–309 Author chain D； PDBConstruct 13–320； UniProt 2–309 Author chain E； PDBConstruct 13–320； UniProt 2–309 Author chain F； PDBConstruct 13–320； UniProt 2–309 Author chain G； PDBConstruct 13–320； UniProt 2–309 Author chain H； PDBConstruct 13–320； UniProt 2–309 Author chain I； PDBConstruct 13–320； UniProt 2–309 Author chain J； PDBConstruct 13–320； UniProt 2–309 Author chain K； PDBConstruct 13–320； UniProt 2–309 Author chain L； PDBConstruct 13–320； UniProt 2–309

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	7c0c
Deposition date deposition_date	2020-05-01
Structure title title	Crystal structure of Azospirillum brasilense L-2-keto-3-deoxyarabonate dehydratase (apo form)
Keywords keywords	L-2-keto-3-deoxyarabonate dehydratase, 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.

7c0c__assembly_2__model_1

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

Download this curve (.dat)

7c0c__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7c0c__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	31.54 Å
Rg (electron density)	30.29 Å
Total Rg	31.01 Å
Atom count	9346
Residues	1214
Excluded volume	165630 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7c0c__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7c0c__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7c0c__assembly_3__model_1`	tetrameric （4）	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 (2)

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6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d7c0ca_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.0 — automated matches

Domain ID domain_id	d7c0cb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.0 — automated matches

Domain ID domain_id	d7c0cc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.0 — automated matches

Domain ID domain_id	d7c0cd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.0 — automated matches

Domain ID domain_id	d7c0ce_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.0 — automated matches

Domain ID domain_id	d7c0cf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.0 — automated matches

Domain ID domain_id	d7c0cg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.0 — automated matches

Domain ID domain_id	d7c0ch_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.0 — automated matches

Domain ID domain_id	d7c0ci_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.0 — automated matches

Domain ID domain_id	d7c0cj_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.0 — automated matches

Domain ID domain_id	d7c0ck_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.0 — automated matches

Domain ID domain_id	d7c0cl_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.0 — automated matches

CATH v4.4 (10 domains)

Domain ID domain_id	7c0cA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	7c0cC01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	7c0cD01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	7c0cE01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	7c0cF01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	7c0cG01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	7c0cH01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	7c0cI01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	7c0cJ01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	7c0cL01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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Unit-cell length a length_a	75.394 Å
Unit-cell length b length_b	81.812 Å
Unit-cell length c length_c	144.419 Å
Unit-cell angle α angle_alpha	85.47 °
Unit-cell angle β angle_beta	87.86 °
Unit-cell angle γ angle_gamma	75.62 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	40.440 Å
R factor r_factor	0.2547
R_work r_work	0.2524
R_free r_free	0.2974

Description description	L-2-keto-3-deoxyarabonate dehydratase
Molecular weight formula_weight	35069.8 kDa
EC 编号 ec_number	4.2.1.43
Source method src_method	man
Copy count entity_count	12

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	29770

Crystal structure of Azospirillum brasilense L-2-keto-3-deoxyarabonate dehydratase (apo form)

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

L-2-keto-3-deoxyarabonate dehydratase

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

7c0c__assembly_2__model_1

7c0c__assembly_2__model_1 | I(q)

7c0c__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (12 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Source organism organism	Azospirillum brasilense
NCBI taxonomy ID ncbi_taxonomy_id	192
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1764

Crystal structure of Azospirillum brasilense L-2-keto-3-deoxyarabonate dehydratase (apo form)

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

L-2-keto-3-deoxyarabonate dehydratase

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

7c0c__assembly_2__model_1

7c0c__assembly_2__model_1 | I(q)

7c0c__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (12 domains)

CATH v4.4 (10 domains)

7. Citations (1)