1h48

The structure of 2C-Methyl-D-erythritol 2,4-cyclodiphosphate synthase in complex with CMP and product

Method: X-RAY DIFFRACTION

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

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

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE × 3 ZINC ION × 3 CYTIDINE-5'-MONOPHOSPHATE × 3 MANGANESE (II) ION × 1 GERANYL DIPHOSPHATE × 1 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE × 3 ZINC ION × 3 CYTIDINE-5'-MONOPHOSPHATE × 3 MANGANESE (II) ION × 1 GERANYL DIPHOSPHATE × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ISPF_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–161； UniProt 1–159 Author chain B； PDBConstruct 3–161； UniProt 1–159 Author chain C； PDBConstruct 3–161； UniProt 1–159 Author chain D； PDBConstruct 3–161； UniProt 1–159 Author chain E； PDBConstruct 3–161； UniProt 1–159 Author chain F； PDBConstruct 3–161； UniProt 1–159

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	1h48
Deposition date deposition_date	2003-02-24
Structure title title	The structure of 2C-Methyl-D-erythritol 2,4-cyclodiphosphate synthase in complex with CMP and product
Keywords keywords	SYNTHASE, ISOPRENOID, LYASE, ISOPRENE BIOSYNTHESIS; SYNTHASE
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.

1h48__assembly_1__model_1

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

Download this curve (.dat)

1h48__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1h48__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.53 Å
Rg (electron density)	20.51 Å
Total Rg	21.27 Å
Atom count	3676
Residues	474
Excluded volume	65464 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1h48__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1h48__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 (7)

Entity 1 Entity 1 polymer

Description description	2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE
Molecular weight formula_weight	17162.8 kDa
EC 编号 ec_number	4.6.1.12
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	7665

LEMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIKATK

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	511693
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE
Molecular weight formula_weight	278.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	CYTIDINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	323.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	GERANYL DIPHOSPHATE
Molecular weight formula_weight	314.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	187

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1h48a1
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	d1h48a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1h48b1
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	d1h48b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1h48c1
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	d1h48c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1h48d1
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	d1h48d2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1h48e1
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	d1h48e2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1h48f1
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	d1h48f2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	1h48A00
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	1h48B00
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	1h48C00
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	1h48D00
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	1h48E00
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	1h48F00
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	198.122 Å
Unit-cell length b length_b	150.287 Å
Unit-cell length c length_c	57.559 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.52 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2040
R_work r_work	0.2020
R_free r_free	0.2360

The structure of 2C-Methyl-D-erythritol 2,4-cyclodiphosphate synthase in complex with CMP and product

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

1h48__assembly_1__model_1

1h48__assembly_1__model_1 | I(q)

1h48__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)

The structure of 2C-Methyl-D-erythritol 2,4-cyclodiphosphate synthase in complex with CMP and product

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

1h48__assembly_1__model_1

1h48__assembly_1__model_1 | I(q)

1h48__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)