SAXSdb — 3fpi

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

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

Yersinia pestis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	CYTIDINE-5'-TRIPHOSPHATE × 3 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3 CHLORIDE ION × 3 SULFATE ION × 3 MAGNESIUM ION × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ISPF_YERPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–165； UniProt 1–162

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	3fpi
Deposition date deposition_date	2009-01-05
Structure title title	Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase IspF complexed with Cytidine Triphosphate
Keywords keywords	;CSGID, alpha-beta sandwich, Isoprene biosynthesis, Lyase, Metal-binding, Structural Genomics, Structural Genomics of National Institute of Allergy and Infectious Diseases, Center for Structural Genomics of Infectious Diseases ;; 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.

3fpi__assembly_1__model_1

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

Download this curve (.dat)

3fpi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fpi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.17 Å
Rg (electron density)	20.97 Å
Total Rg	21.85 Å
Atom count	3745
Residues	471
Excluded volume	66489 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fpi__assembly_1__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	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Molecular weight formula_weight	17663.5 kDa
EC 编号 ec_number	4.6.1.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1341

SNAMRIGHGFDVHKFGENGSGPLIIGGVRIPYEKGLLAHSDGDVALHAATDALLGAAALGDIGKLFPDTDPAFKGADSRGLLREAYRRILAKGYKLGNLDITIIAQAPKMAPHIPQMRVNLAEDLQCHMDDINVKATTTEQLGFTGRGEGIACEAVVLLVNVEQG

Source Source

Source organism organism	Yersinia pestis
NCBI taxonomy ID ncbi_taxonomy_id	214092
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CYTIDINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	483.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	76

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3fpia1
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	d3fpia2
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 (1 domains)

Domain ID domain_id	3fpiA00
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	145.639 Å
Unit-cell length b length_b	145.639 Å
Unit-cell length c length_c	145.639 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	I 21 3
Space-group number int_tables_number	199
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	34.330 Å
R factor r_factor	0.1720
R_work r_work	0.1700
R_free r_free	0.1990

Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase IspF complexed with Cytidine Triphosphate

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

3fpi__assembly_1__model_1

3fpi__assembly_1__model_1 | I(q)

3fpi__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase IspF complexed with Cytidine Triphosphate

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

3fpi__assembly_1__model_1

3fpi__assembly_1__model_1 | I(q)

3fpi__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)