1iv1

Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase

Method: X-RAY DIFFRACTION

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

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Thermus thermophilus

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ISPF_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–152； UniProt 1–152 Author chain B； PDBConstruct 1–152； UniProt 1–152 Author chain C； PDBConstruct 1–152； UniProt 1–152 Author chain D； PDBConstruct 1–152； UniProt 1–152 Author chain E； PDBConstruct 1–152； UniProt 1–152 Author chain F； PDBConstruct 1–152； UniProt 1–152

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	1iv1
Deposition date deposition_date	2002-03-11
Structure title title	Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase
Keywords keywords	isoprenoid, non-mevalonate, synthase, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, 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.

1iv1__assembly_1__model_1

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

Download this curve (.dat)

1iv1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1iv1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.90 Å
Rg (electron density)	20.67 Å
Total Rg	21.58 Å
Atom count	3456
Residues	450
Excluded volume	61762 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1iv1__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1iv1__assembly_2__model_1`	trimeric （3）	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) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1iv1a_
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	d1iv1b_
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	d1iv1c_
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	d1iv1d_
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	d1iv1e_
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	d1iv1f_
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 (6 domains)

Domain ID domain_id	1iv1A00
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	1iv1B00
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	1iv1C00
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	1iv1D00
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	1iv1E00
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	1iv1F00
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	105.828 Å
Unit-cell length b length_b	105.828 Å
Unit-cell length c length_c	148.674 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	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2280
R_free r_free	0.3140

Description description	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Molecular weight formula_weight	16544.1 kDa
EC 编号 ec_number	4.6.1.12
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,D,B,E,F
Atom count atom_count	7264

Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase

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

2-C-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

1iv1__assembly_1__model_1

1iv1__assembly_1__model_1 | I(q)

1iv1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
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	352

Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase

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

2-C-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

1iv1__assembly_1__model_1

1iv1__assembly_1__model_1 | I(q)

1iv1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)