SAXSdb — 2v9d

▼

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

YAGE

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YAGE_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–327； UniProt 3–309 Author chain B； PDBConstruct 21–327； UniProt 3–309 Author chain C； PDBConstruct 21–327； UniProt 3–309 Author chain D； PDBConstruct 21–327； UniProt 3–309

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2v9d
Deposition date deposition_date	2007-08-23
Structure title title	Crystal Structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. coli K12
Keywords keywords	DIHYDRODIPICOLINIC ACID SYNTHASE, N-ACETYL NEURAMINATE LYASE, NAL, LYASE, DHDPS, PROPHAGE; LYASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2v9d__assembly_1__model_1

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

Download this curve (.dat)

2v9d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2v9d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.30 Å
Rg (electron density)	31.13 Å
Total Rg	31.92 Å
Atom count	9011
Residues	1180
Excluded volume	161910 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2v9d__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2v9da_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.0 — automated matches

Domain ID domain_id	d2v9db_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.0 — automated matches

Domain ID domain_id	d2v9dc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.0 — automated matches

Domain ID domain_id	d2v9dd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2v9dA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	2v9dB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	2v9dC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	2v9dD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

▶

Unit-cell length a length_a	56.279 Å
Unit-cell length b length_b	149.806 Å
Unit-cell length c length_c	78.967 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.42 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	36.350 Å
R factor r_factor	0.1680
R_work r_work	0.1660
R_free r_free	0.2180

Description description	YAGE
Molecular weight formula_weight	37247.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9660

Crystal Structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. coli K12

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

YAGE

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

2v9d__assembly_1__model_1

2v9d__assembly_1__model_1 | I(q)

2v9d__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	83333
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	649

Crystal Structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. coli K12

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

YAGE

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

2v9d__assembly_1__model_1

2v9d__assembly_1__model_1 | I(q)

2v9d__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)