3a9s

X-ray Structure of Bacillus pallidus D-Arabinose Isomerase Complex with Glycerol

Method: X-RAY DIFFRACTION

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

D-arabinose isomerase

Geobacillus pallidus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	GLYCEROL × 12 MANGANESE (II) ION × 12 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C0SSE7_9BACI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–595； UniProt 1–595 Author chain B； PDBConstruct 1–595； UniProt 1–595 Author chain C； PDBConstruct 1–595； UniProt 1–595

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	3a9s
Deposition date deposition_date	2009-11-05
Structure title title	X-ray Structure of Bacillus pallidus D-Arabinose Isomerase Complex with Glycerol
Keywords keywords	Rossmann fold, beta barrel, Carbohydrate metabolism, Cytoplasm, Fucose metabolism, Isomerase, Manganese, Metal-binding; 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.

3a9s__assembly_1__model_1

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

Download this curve (.dat)

3a9s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3a9s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.99 Å
Rg (electron density)	43.06 Å
Total Rg	43.41 Å
Atom count	27708
Residues	3534
Excluded volume	492770 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3a9s__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	D-arabinose isomerase
Molecular weight formula_weight	66220.0 kDa
EC 编号 ec_number	5.3.1.3
Mutation mutation	E225G, N589K, F590L
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	15445

MAKDPRYVGNLPKIGIRPTIDGRRKGVRESLEETTMNMAKAVAKLLEENVFYYNGQPVECVIADTCIGGVKEAAEAAEKFAREGVGVSITVTPCWCYGTETMDMDPHIPKAVWGFNGTERPGAVYLAAVLAGYNQKGLPAFGIYGKDVQDAGDTNIPEDVKEKLIRFAKAGLAVAMMKGKSYLSIGSVSMGIAGSVVQEDFFQNYLGMRNEYVDMSEFVRRIELGIYDKEEYERALKWVKENCKVGPDNNRDGFKRTEEQKEKDWEISVKMALIARDLMVGNKKLEEMGYGEEALGRNAIVAGFQGQRQWTDYFPNGDFMETILNSSFDWNGKRAPYIFATENDNLNGISMLFGYLLTNTAQIFADVRTYWSPEAVKRVTGYTLEGRAANGIIHLINSGAAALDGTGEQTKDGKPVIKPYYELTDEDIKKCLEATQFRPASTEYFRGGGYSTDFLTKGGMPVTISRLNIVKGLGPVLQIAEGYTVDLPEEVHDVLDKRTDPTWPTTWFVPNLTGEGAFKDVYSVMNNWGANHCSISYGHIGADLITLASILRIPVNMHNVPEEKIFRPDAWSMFGTKDLEGADYRACKKLGPIYK

Source Source

Source organism organism	Geobacillus pallidus
NCBI taxonomy ID ncbi_taxonomy_id	33936
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1579

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3a9sa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.85 — FucI/AraA N-terminal and middle domains
Superfamily Superfamily superfamily	c.85.1 — FucI/AraA N-terminal and middle domains
Family Family family	c.85.1.0 — automated matches

Domain ID domain_id	d3a9sa2
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.2 — FucI/AraA C-terminal domain-like
Family Family family	b.43.2.0 — automated matches

Domain ID domain_id	d3a9sb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.85 — FucI/AraA N-terminal and middle domains
Superfamily Superfamily superfamily	c.85.1 — FucI/AraA N-terminal and middle domains
Family Family family	c.85.1.0 — automated matches

Domain ID domain_id	d3a9sb2
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.2 — FucI/AraA C-terminal domain-like
Family Family family	b.43.2.0 — automated matches

Domain ID domain_id	d3a9sc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.85 — FucI/AraA N-terminal and middle domains
Superfamily Superfamily superfamily	c.85.1 — FucI/AraA N-terminal and middle domains
Family Family family	c.85.1.0 — automated matches

Domain ID domain_id	d3a9sc2
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.2 — FucI/AraA C-terminal domain-like
Family Family family	b.43.2.0 — automated matches

CATH v4.4 (9 domains)

Domain ID domain_id	3a9sA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1070 —

Domain ID domain_id	3a9sA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	275 — L-fucose Isomerase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — L-fucose Isomerase; Chain A, domain 2

Domain ID domain_id	3a9sA03
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	14 — L-fucose Isomerase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — L-fucose/L-arabinose isomerase, C-terminal

Domain ID domain_id	3a9sB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1070 —

Domain ID domain_id	3a9sB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	275 — L-fucose Isomerase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — L-fucose Isomerase; Chain A, domain 2

Domain ID domain_id	3a9sB03
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	14 — L-fucose Isomerase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — L-fucose/L-arabinose isomerase, C-terminal

Domain ID domain_id	3a9sC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1070 —

Domain ID domain_id	3a9sC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	275 — L-fucose Isomerase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — L-fucose Isomerase; Chain A, domain 2

Domain ID domain_id	3a9sC03
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	14 — L-fucose Isomerase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — L-fucose/L-arabinose isomerase, C-terminal

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Unit-cell length a length_a	144.317 Å
Unit-cell length b length_b	127.271 Å
Unit-cell length c length_c	110.315 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	12

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	40.700 Å
R factor r_factor	0.1680
R_work r_work	0.1680
R_free r_free	0.1870

X-ray Structure of Bacillus pallidus D-Arabinose Isomerase Complex with Glycerol

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

D-arabinose isomerase

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

3a9s__assembly_1__model_1

3a9s__assembly_1__model_1 | I(q)

3a9s__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (1)

X-ray Structure of Bacillus pallidus D-Arabinose Isomerase Complex with Glycerol

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

D-arabinose isomerase

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

3a9s__assembly_1__model_1

3a9s__assembly_1__model_1 | I(q)

3a9s__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (1)