4r1q

Crystal Structure of Thermophilic Geobacillus kaustophilus L-Arabinose isomerase in complex with L-arabitol

Method: X-RAY DIFFRACTION

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

L-arabinose isomerase

Geobacillus kaustophilus HTA426

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARAA_GEOKA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–497； UniProt 1–496 Author chain B； PDBConstruct 2–497； UniProt 1–496 Author chain C； PDBConstruct 2–497； UniProt 1–496 Author chain D； PDBConstruct 2–497； UniProt 1–496 Author chain E； PDBConstruct 2–497； UniProt 1–496 Author chain F； PDBConstruct 2–497； UniProt 1–496

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	4r1q
Deposition date deposition_date	2014-08-07
Structure title title	Crystal Structure of Thermophilic Geobacillus kaustophilus L-Arabinose isomerase in complex with L-arabitol
Keywords keywords	Hexamer, Thermophile, thermostable, AI fold, 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.

4r1q__assembly_1__model_1

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

Download this curve (.dat)

4r1q__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4r1q__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.07 Å
Rg (electron density)	42.22 Å
Total Rg	42.60 Å
Atom count	23743
Residues	2972
Excluded volume	420520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4r1q__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	L-arabinose isomerase
Molecular weight formula_weight	56304.9 kDa
EC 编号 ec_number	5.3.1.4
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	25396

MMLSLRPYEFWFVTGSQHLYGEEALKQVEEHSRIMVNEWNRDSVFPFPFVFKSVVTTPEEIRRVCLEANASEQCAGVVTWMHTFSPAKMWIGGLLELRKPLLHLHTQFNRDIPWDSIDMDFMNLNQSAHGDREYGFIGARMGVARKVVVGHWEDPEVRERLAKWMRTAVAFAESRNLKVARFGDNMREVAVTEGDKVGAQIQFGWSVNGYGIGDLVQYIRDVSEQKVNELLDEYEELYDIVPAGRQEGPVRESIREQARIELGLKAFLQDGNFTAFTTTFEDLHGMKQLPGLAVQRLMAEGYGFGGEGDWKTAALVRLMKVMADGKGTSFMEDYTYHFEPGNELILGAHMLEVCPTIAATRPRVEVHPLSIGGKEDPARLVFDGGEGAAVNASLIDLGHRFRLIVNEVDAVKPEHDMPKLPVARILWKPRPSLRDSAEAWILAGGAHHTCFSFAVTTEQLQDFAEMAGIECVVINEHTSVSSFKNELKWNEVFWRGR

Source Source

Source organism organism	Geobacillus kaustophilus HTA426
NCBI taxonomy ID ncbi_taxonomy_id	235909
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	L-arabinitol
Molecular weight formula_weight	152.1 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	1645

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d4r1qa1
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	d4r1qa2
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	d4r1qb1
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	d4r1qb2
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	d4r1qc1
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	d4r1qc2
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	d4r1qd1
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	d4r1qd2
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	d4r1qe1
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	d4r1qe2
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	d4r1qf1
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	d4r1qf2
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 (6 domains)

Domain ID domain_id	4r1qA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10940 —

Domain ID domain_id	4r1qB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10940 —

Domain ID domain_id	4r1qC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10940 —

Domain ID domain_id	4r1qD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10940 —

Domain ID domain_id	4r1qE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10940 —

Domain ID domain_id	4r1qF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10940 —

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Unit-cell length a length_a	118.514 Å
Unit-cell length b length_b	146.263 Å
Unit-cell length c length_c	215.677 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.248 Å
Low-resolution limit resolution_low	49.079 Å
R factor r_factor	0.1562
R_work r_work	0.1538
R_free r_free	0.2012

Crystal Structure of Thermophilic Geobacillus kaustophilus L-Arabinose isomerase in complex with L-arabitol

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

L-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

4r1q__assembly_1__model_1

4r1q__assembly_1__model_1 | I(q)

4r1q__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) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of Thermophilic Geobacillus kaustophilus L-Arabinose isomerase in complex with L-arabitol

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

L-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

4r1q__assembly_1__model_1

4r1q__assembly_1__model_1 | I(q)

4r1q__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) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)