SAXSdb — 3es1

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

Cupin 2, conserved barrel domain protein

Novosphingobium aromaticivorans DSM 12444

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4XEC0_NOVAD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–172； UniProt 1–171

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	3es1
Deposition date deposition_date	2008-10-03
Structure title title	Crystal structure of protein with a cupin-like fold and unknown function (YP_001165807.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.91 A resolution
Keywords keywords	;YP_001165807.1, protein with a cupin-like fold and unknown function, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, Cupin domain, unknown function ;; structural genomics, unknown function
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.

3es1__assembly_1__model_1

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

Download this curve (.dat)

3es1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3es1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.48 Å
Rg (electron density)	19.16 Å
Total Rg	20.03 Å
Atom count	2476
Residues	320
Excluded volume	43609 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3es1__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 (3)

Entity 1 Entity 1 polymer

Description description	Cupin 2, conserved barrel domain protein
Molecular weight formula_weight	18955.6 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	1461

GMSEALSDSGLPPVQRVVTGHDAHGRAVFKSEDVTPTRMIPSGDASFLLVWTTATVPADNNDETDGRQREAGLTLDGGSVIRVVDMLPGKESPMHRTNSIDYGIVLEGEIELELDDGAKRTVRQGGIIVQRGTNHLWRNTTDKPCRIAFILIEAPAYLHNGQPLPEDKPDHK

Source Source

Source organism organism	Novosphingobium aromaticivorans DSM 12444
NCBI taxonomy ID ncbi_taxonomy_id	279238
Host organism host_organism	Escherichia Coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	188

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3es1A01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	3es1A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

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Unit-cell length a length_a	78.330 Å
Unit-cell length b length_b	78.330 Å
Unit-cell length c length_c	107.320 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	1.910 Å
Low-resolution limit resolution_low	28.665 Å
R factor r_factor	0.1720
R_work r_work	0.1700
R_free r_free	0.2050

Crystal structure of protein with a cupin-like fold and unknown function (YP_001165807.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.91 A resolution

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

Cupin 2, conserved barrel domain protein

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

3es1__assembly_1__model_1

3es1__assembly_1__model_1 | I(q)

3es1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of protein with a cupin-like fold and unknown function (YP_001165807.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.91 A resolution

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

Cupin 2, conserved barrel domain protein

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

3es1__assembly_1__model_1

3es1__assembly_1__model_1 | I(q)

3es1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)