SAXSdb — 5yxc

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

Metal-binding protein ZinT

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 CITRIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 CITRIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ZINT_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–216； UniProt 1–216 Author chain B； PDBConstruct 1–216； UniProt 1–216

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	5yxc
Deposition date deposition_date	2017-12-04
Structure title title	Crystal structure of Zinc binding protein ZinT in complex with citrate from E. coli
Keywords keywords	Zinc binding protein, complex, citrate, METAL BINDING PROTEIN; METAL BINDING PROTEIN
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.

5yxc__assembly_1__model_1

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

Download this curve (.dat)

5yxc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5yxc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.59 Å
Rg (electron density)	16.48 Å
Total Rg	17.59 Å
Atom count	2966
Residues	187
Excluded volume	27045 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5yxc__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5yxc__assembly_2__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	Metal-binding protein ZinT
Molecular weight formula_weight	24795.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6425

MAIRLYKLAVALGVFIVSAPAFSHGHHSHGKPLTEVEQKAANGVFDDANVQNRTLSDWDGVWQSVYPLLQSGKLDPVFQKKADADKTKTFAEIKDYYHKGYATDIEMIGIEDGIVEFHRNNETTSCKYDYDGYKILTYKSGKKGVRYLFECKDPESKAPKYIQFSDHIIAPRKSSHFHIFMGNDSQQSLLNEMENWPTYYPYQLSSEEVVEEMMSH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	493

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5yxca_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.4 — Hypothetical protein YodA

Domain ID domain_id	d5yxcb_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.4 — Hypothetical protein YodA

CATH v4.4 (2 domains)

Domain ID domain_id	5yxcA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

Domain ID domain_id	5yxcB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

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Unit-cell length a length_a	41.040 Å
Unit-cell length b length_b	65.866 Å
Unit-cell length c length_c	73.536 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.35 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.763 Å
Low-resolution limit resolution_low	41.029 Å
R factor r_factor	0.1898
R_work r_work	0.1875
R_free r_free	0.2341

Crystal structure of Zinc binding protein ZinT in complex with citrate from E. coli

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

Metal-binding protein ZinT

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

5yxc__assembly_1__model_1

5yxc__assembly_1__model_1 | I(q)

5yxc__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Zinc binding protein ZinT in complex with citrate from E. coli

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

Metal-binding protein ZinT

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

5yxc__assembly_1__model_1

5yxc__assembly_1__model_1 | I(q)

5yxc__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)