SAXSdb — 2re3

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

Uncharacterized protein

Silicibacter pomeroyi DSS-3

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5LWU5_SILPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–194； UniProt 1–193 Author chain B； PDBConstruct 2–194； UniProt 1–193

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	2re3
Deposition date deposition_date	2007-09-25
Structure title title	CRYSTAL STRUCTURE OF a DUF1285 family protein (SPO_0140) FROM SILICIBACTER POMEROYI DSS-3 AT 2.50 A RESOLUTION
Keywords keywords	STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, UNKNOWN FUNCTION; 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.

2re3__assembly_2__model_1

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

Download this curve (.dat)

2re3__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2re3__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	18.89 Å
Rg (electron density)	18.05 Å
Total Rg	18.97 Å
Atom count	1420
Residues	179
Excluded volume	25257 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2re3__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2re3__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 (3)

Entity 1 Entity 1 polymer

Description description	Uncharacterized protein
Molecular weight formula_weight	21607.6 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	3144

GMSGQKPVKPSADGLLASARAIKSKGPAPVHLWNPPFNGDIDMRIARDGTWFYQGTPINRPAMVRLFSSILKREEDRFYLVTPVEKVGIRVDDAPFVAVDVEVAGQGRKQVLTFTTHVGDSAVAGEGNPIRMAQDPATGEPAPYVHVRAGLEALIDRKSFYRLMDLGEIEDGWFGLWSSGSFFPLMTVEELERG

Source Source

Source organism organism	Silicibacter pomeroyi DSS-3
NCBI taxonomy ID ncbi_taxonomy_id	246200
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	186

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2re3A01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	540 — duf1285 like fold
Homologous superfamily homologous superfamily	10 — duf1285 like domain

Domain ID domain_id	2re3A02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	270 — duf1285 protein fold
Homologous superfamily homologous superfamily	10 — duf1285 protein

Domain ID domain_id	2re3A03
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2re3B01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	540 — duf1285 like fold
Homologous superfamily homologous superfamily	10 — duf1285 like domain

Domain ID domain_id	2re3B02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	270 — duf1285 protein fold
Homologous superfamily homologous superfamily	10 — duf1285 protein

Domain ID domain_id	2re3B03
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	75.370 Å
Unit-cell length b length_b	75.370 Å
Unit-cell length c length_c	182.687 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	29.488 Å
R factor r_factor	0.2170
R_work r_work	0.2150
R_free r_free	0.2580

CRYSTAL STRUCTURE OF a DUF1285 family protein (SPO_0140) FROM SILICIBACTER POMEROYI DSS-3 AT 2.50 A RESOLUTION

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

Uncharacterized 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

2re3__assembly_2__model_1

2re3__assembly_2__model_1 | I(q)

2re3__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 (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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF a DUF1285 family protein (SPO_0140) FROM SILICIBACTER POMEROYI DSS-3 AT 2.50 A RESOLUTION

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

Uncharacterized 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

2re3__assembly_2__model_1

2re3__assembly_2__model_1 | I(q)

2re3__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 (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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)