SAXSdb — 3f1c

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

Putative 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2

Listeria monocytogenes str. 4b F2365

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ISPD2_LISMF
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–238； UniProt 2–236 Author chain B； PDBConstruct 4–238； UniProt 2–236

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	3f1c
Deposition date deposition_date	2008-10-27
Structure title title	CRYSTAL STRUCTURE OF 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase from Listeria monocytogenes
Keywords keywords	;STRUCTURAL GENOMICS, TRANSFERASE, PSI-2, PROTEIN STRUCTURE INITIATIVE, NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM, NYSGXRC, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, Isoprene biosynthesis, Nucleotidyltransferase ;; TRANSFERASE
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.

3f1c__assembly_1__model_1

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

Download this curve (.dat)

3f1c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3f1c__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.89 Å
Rg (electron density)	25.09 Å
Total Rg	25.90 Å
Atom count	3658
Residues	459
Excluded volume	65681 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3f1c__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 (2)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3f1ca1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.0 — automated matches

Domain ID domain_id	d3f1ca2
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	d3f1cb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.0 — automated matches

Domain ID domain_id	d3f1cb2
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 (2 domains)

Domain ID domain_id	3f1cA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	3f1cB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

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Unit-cell length a length_a	157.202 Å
Unit-cell length b length_b	45.938 Å
Unit-cell length c length_c	79.007 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.89 °
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	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2419
R_work r_work	0.2407
R_free r_free	0.2767

Description description	Putative 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2
Molecular weight formula_weight	27927.0 kDa
EC 编号 ec_number	2.7.7.60
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3801

CRYSTAL STRUCTURE OF 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase from Listeria monocytogenes

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

Putative 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2

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

3f1c__assembly_1__model_1

3f1c__assembly_1__model_1 | I(q)

3f1c__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Listeria monocytogenes str. 4b F2365
NCBI taxonomy ID ncbi_taxonomy_id	265669
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	67

CRYSTAL STRUCTURE OF 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase from Listeria monocytogenes

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

Putative 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2

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

3f1c__assembly_1__model_1

3f1c__assembly_1__model_1 | I(q)

3f1c__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)