SAXSdb — 2oel

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

2,3-diketo-5-methylthiopentyl-1-phosphate enolase

Geobacillus kaustophilus

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTNW_GEOKA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–413； UniProt 1–413 Author chain B； PDBConstruct 1–413； UniProt 1–413

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	2oel
Deposition date deposition_date	2006-12-30
Structure title title	Crystal structure of a rubisco-like protein from Geobacillus kaustophilus liganded with Mg2+ and HCO3- ions
Keywords keywords	;Rubisco-like protein, "enolase", 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.

2oel__assembly_1__model_1

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

Download this curve (.dat)

2oel__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2oel__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.17 Å
Rg (electron density)	27.78 Å
Total Rg	28.62 Å
Atom count	6348
Residues	822
Excluded volume	113770 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2oel__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	2,3-diketo-5-methylthiopentyl-1-phosphate enolase
Molecular weight formula_weight	45003.6 kDa
EC 编号 ec_number	5.3.2.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7016

MSAVMATYLLHDETDIRKKAEGIALGLTIGTWTDLPALEQEQLRKHKGEVVAIEELGESERVNAYFGKRLKRAIVKIAYPTVNFSADLPALLVTTFGKLSLDGEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVHNRPLLMSIFKGMIGRDLAYLTSELKKQALGGVDLVKDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGKTFALKDKAKRAAELGADVLLFNVFAYGLDVLQALREDEEIAVPIMAHPAFSGAVTPSEFYGVAPSLWLGKLLRLAGADFVLFPSPYGSVALEREQALGIARALTDDQEPFARAFPVPSAGIHPGLVPLIIRDFGLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGVVEVEA

Source Source

Source organism organism	Geobacillus kaustophilus
NCBI taxonomy ID ncbi_taxonomy_id	1462
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CARBONATE ION
Molecular weight formula_weight	60.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	668

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2oela1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family family	d.58.9.0 — automated matches

Domain ID domain_id	d2oela2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
Family Family family	c.1.14.0 — automated matches

Domain ID domain_id	d2oelb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family family	d.58.9.0 — automated matches

Domain ID domain_id	d2oelb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
Family Family family	c.1.14.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2oelA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	150 — RuBisCO large subunit, N-terminal domain

Domain ID domain_id	2oelA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain

Domain ID domain_id	2oelB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	150 — RuBisCO large subunit, N-terminal domain

Domain ID domain_id	2oelB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain

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Unit-cell length a length_a	130.700 Å
Unit-cell length b length_b	59.014 Å
Unit-cell length c length_c	109.476 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	24.830 Å
R factor r_factor	0.1960
R_work r_work	0.1960
R_free r_free	0.2200

Crystal structure of a rubisco-like protein from Geobacillus kaustophilus liganded with Mg2+ and HCO3- ions

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

2,3-diketo-5-methylthiopentyl-1-phosphate enolase

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

2oel__assembly_1__model_1

2oel__assembly_1__model_1 | I(q)

2oel__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a rubisco-like protein from Geobacillus kaustophilus liganded with Mg2+ and HCO3- ions

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

2,3-diketo-5-methylthiopentyl-1-phosphate enolase

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

2oel__assembly_1__model_1

2oel__assembly_1__model_1 | I(q)

2oel__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)