SAXSdb — 1xvx

▼

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

YfuA

Yersinia enterocolitica

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FE (III) ION × 1 ZINC ION × 5 CARBONATE ION × 1 1,2-ETHANEDIOL × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q56925_YEREN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–312； UniProt 27–338

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	1xvx
Deposition date deposition_date	2004-10-28
Structure title title	Crystal Structure of iron-loaded Yersinia enterocolitica YfuA
Keywords keywords	periplasmic iron binding protein, iron binding protein; iron binding protein
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.

1xvx__assembly_1__model_1

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

Download this curve (.dat)

1xvx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xvx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.30 Å
Rg (electron density)	19.21 Å
Total Rg	20.24 Å
Atom count	2398
Residues	311
Excluded volume	42713 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xvx__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	YfuA
Molecular weight formula_weight	33917.2 kDa
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	2879

ESNDSGIVVYNAQHENLVKSWVDGFTKDTGIKVTLRNGGDSELGNQLVQEGSASPADVFLTENSPAMVLVDNAKLFAPLDAVTQAQVAQEYRPEHGRWTGIAARSTVFVYNPEKISEAELPKSIMDLAKPEWKGRWAASPSGADFQAIVSAMLELKGEKATLEWLKAMKTNFTAYKGNSTVMKAVNAGQIDGGVIYHYYRFVDQAKTGENSGKTQLHYFKHQDPGAFVSISGGGVLASSKHPKEAQEFVKWITGKSGQDILRTNNAFEYAVGVDAASNPKLVPLKDLDAPKVEPSKLNSKKVVELMTEAGLL

Source Source

Source organism organism	Yersinia enterocolitica
NCBI taxonomy ID ncbi_taxonomy_id	630
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

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	5

Entity 4 Entity 4 non-polymer

Description description	CARBONATE ION
Molecular weight formula_weight	60.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	477

▼

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1xvxa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

CATH v4.4 (2 domains)

Domain ID domain_id	1xvxA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1xvxA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

▶

Unit-cell length a length_a	108.392 Å
Unit-cell length b length_b	46.951 Å
Unit-cell length c length_c	62.454 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.51 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.530 Å
Low-resolution limit resolution_low	60.860 Å
R factor r_factor	0.1630
R_work r_work	0.1615
R_free r_free	0.1930

Crystal Structure of iron-loaded Yersinia enterocolitica YfuA

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

YfuA

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

1xvx__assembly_1__model_1

1xvx__assembly_1__model_1 | I(q)

1xvx__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of iron-loaded Yersinia enterocolitica YfuA

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

YfuA

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

1xvx__assembly_1__model_1

1xvx__assembly_1__model_1 | I(q)

1xvx__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)