SAXSdb — 1jn1

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

2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE

Haemophilus influenzae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	COBALT (II) ION × 4 SULFATE ION × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 12	COBALT (II) ION × 16 SULFATE ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ISPF_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–158； UniProt 1–158 Author chain B； PDBConstruct 1–158； UniProt 1–158 Author chain C； PDBConstruct 1–158； UniProt 1–158

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	1jn1
Deposition date deposition_date	2001-07-21
Structure title title	Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Haemophilus influenzae (HI0671)
Keywords keywords	;2C-METHYL-D-ERYTHRITOL 2, 4-CYCLODIPHOSPHATE SYNTHASE, MECPS, isoprenoid biosynthesis, structural genomics, Structure 2 Function Project, S2F, unknown function ;; STRUCTURAL GENOMICS, unknown function
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.

1jn1__assembly_2__model_1

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

Download this curve (.dat)

1jn1__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1jn1__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	36.06 Å
Rg (electron density)	35.37 Å
Total Rg	36.03 Å
Atom count	14412
Residues	1884
Excluded volume	256520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1jn1__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1jn1__assembly_2__model_1`	dodecameric （12）	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 (3)

Entity 1 Entity 1 polymer

Description description	2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
Molecular weight formula_weight	17216.7 kDa
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	3603

MIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFPDTDMQYKNADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKMRPHIDAMRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIRQ

Source Source

Source organism organism	Haemophilus influenzae
NCBI taxonomy ID ncbi_taxonomy_id	727
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1jn1a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.5 — IpsF-like
Family Family family	d.79.5.1 — IpsF-like

Domain ID domain_id	d1jn1b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.5 — IpsF-like
Family Family family	d.79.5.1 — IpsF-like

Domain ID domain_id	d1jn1c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.5 — IpsF-like
Family Family family	d.79.5.1 — IpsF-like

CATH v4.4 (3 domains)

Domain ID domain_id	1jn1A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	50 — 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Domain ID domain_id	1jn1B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	50 — 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Domain ID domain_id	1jn1C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	50 — 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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Unit-cell length a length_a	112.300 Å
Unit-cell length b length_b	112.300 Å
Unit-cell length c length_c	187.600 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	48

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1980
R_free r_free	0.2900

Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Haemophilus influenzae (HI0671)

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

2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE

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

1jn1__assembly_2__model_1

1jn1__assembly_2__model_1 | I(q)

1jn1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (2)

Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Haemophilus influenzae (HI0671)

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

2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE

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

1jn1__assembly_2__model_1

1jn1__assembly_2__model_1 | I(q)

1jn1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (2)