SAXSdb — 4nyo

▼

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

Divalent-cation tolerance protein CutA

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	SODIUM ION × 1 CHLORIDE ION × 4 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 SULFATE ION × 1 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	SODIUM ION × 1 CHLORIDE ION × 4 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 SULFATE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CUTA_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–102； UniProt 1–102 Author chain B； PDBConstruct 1–102； UniProt 1–102 Author chain C； PDBConstruct 1–102； UniProt 1–102 Author chain D； PDBConstruct 1–102； UniProt 1–102 Author chain E； PDBConstruct 1–102； UniProt 1–102 Author chain F； PDBConstruct 1–102； UniProt 1–102

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	4nyo
Deposition date deposition_date	2013-12-11
Structure title title	The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta from Pyrococcus Horikoshii OT3
Keywords keywords	Copper Tolerance, Cuta, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, RSGI, METAL BINDING PROTEIN; METAL 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.

4nyo__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4nyo__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4nyo__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.20 Å
Rg (electron density)	18.96 Å
Total Rg	19.94 Å
Atom count	2659
Residues	303
Excluded volume	47825 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4nyo__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4nyo__assembly_2__model_1`	trimeric （3）	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	Divalent-cation tolerance protein CutA
Molecular weight formula_weight	12399.2 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	6012

MIIVYTTFPDWESAEKVVKTLLKERLIACANLREHRAFYWWEGKIEEDKEVGAILKTREDLWEELKERIKELHPYDVPAIIRIDVDDVNEDYLKWLIEETKK

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	4

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	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	688

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4nyoa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.2 — Divalent ion tolerance proteins CutA (CutA1)

Domain ID domain_id	d4nyob_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.2 — Divalent ion tolerance proteins CutA (CutA1)

Domain ID domain_id	d4nyoc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.2 — Divalent ion tolerance proteins CutA (CutA1)

Domain ID domain_id	d4nyod_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.2 — Divalent ion tolerance proteins CutA (CutA1)

Domain ID domain_id	d4nyoe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.2 — Divalent ion tolerance proteins CutA (CutA1)

Domain ID domain_id	d4nyof_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.2 — Divalent ion tolerance proteins CutA (CutA1)

CATH v4.4 (6 domains)

Domain ID domain_id	4nyoA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	4nyoB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	4nyoC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	4nyoD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	4nyoE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	4nyoF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

▶

Unit-cell length a length_a	93.085 Å
Unit-cell length b length_b	124.250 Å
Unit-cell length c length_c	50.458 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	36.100 Å
R factor r_factor	0.1890
R_work r_work	0.1890
R_free r_free	0.2250

The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta from Pyrococcus Horikoshii OT3

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

Divalent-cation tolerance protein CutA

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

4nyo__assembly_2__model_1

4nyo__assembly_2__model_1 | I(q)

4nyo__assembly_2__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta from Pyrococcus Horikoshii OT3

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

Divalent-cation tolerance protein CutA

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

4nyo__assembly_2__model_1

4nyo__assembly_2__model_1 | I(q)

4nyo__assembly_2__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)