SAXSdb — 3dcx

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

Protein of Unknown Function (DUF1696) with Pleckstrin-homology Domains

Shewanella loihica PV-4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	(4S)-2-METHYL-2,4-PENTANEDIOL × 7 CHLORIDE ION × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A3QB43_SHELP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–117； UniProt 9–124 Author chain B； PDBConstruct 2–117； UniProt 9–124 Author chain C； PDBConstruct 2–117； UniProt 9–124 Author chain D； PDBConstruct 2–117； UniProt 9–124 Author chain E； PDBConstruct 2–117； UniProt 9–124

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	3dcx
Deposition date deposition_date	2008-06-04
Structure title title	Crystal structure of a duf1696 family protein with a pleckstrin-homology domain (shew_0819) from shewanella loihica pv-4 at 2.00 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.

3dcx__assembly_1__model_1

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

Download this curve (.dat)

3dcx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dcx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.63 Å
Rg (electron density)	26.28 Å
Total Rg	27.45 Å
Atom count	4423
Residues	546
Excluded volume	80225 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dcx__assembly_1__model_1`	pentameric （5）	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	Protein of Unknown Function (DUF1696) with Pleckstrin-homology Domains
Molecular weight formula_weight	13109.6 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	4860

GGNAAEVNLDELAQELGPIMGDNEQLALAYRVIRDMFVFTNKRLILIDKQGVTGKKVSYHSVPYKAITHFEVETAGTFDMDAELKLWISGQKDPLVKELKKGTDVVGIQKTIANFSL

Source Source

Source organism organism	Shewanella loihica PV-4
NCBI taxonomy ID ncbi_taxonomy_id	323850
Host organism host_organism	Escherichia Coli

Entity 2 Entity 2 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	7

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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	322

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3dcxa1
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.13 — BPHL domain

Domain ID domain_id	d3dcxa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3dcxb_
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.13 — BPHL domain

Domain ID domain_id	d3dcxc_
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.13 — BPHL domain

Domain ID domain_id	d3dcxd_
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.13 — BPHL domain

Domain ID domain_id	d3dcxe_
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.13 — BPHL domain

CATH v4.4 (5 domains)

Domain ID domain_id	3dcxA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	50 — Bacterial Pleckstrin homology domain

Domain ID domain_id	3dcxB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	50 — Bacterial Pleckstrin homology domain

Domain ID domain_id	3dcxC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	50 — Bacterial Pleckstrin homology domain

Domain ID domain_id	3dcxD00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	50 — Bacterial Pleckstrin homology domain

Domain ID domain_id	3dcxE00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	50 — Bacterial Pleckstrin homology domain

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Unit-cell length a length_a	61.070 Å
Unit-cell length b length_b	75.320 Å
Unit-cell length c length_c	139.400 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	20

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	29.828 Å
R factor r_factor	0.1860
R_work r_work	0.1840
R_free r_free	0.2270

Crystal structure of a duf1696 family protein with a pleckstrin-homology domain (shew_0819) from shewanella loihica pv-4 at 2.00 A resolution

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

Protein of Unknown Function (DUF1696) with Pleckstrin-homology Domains

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

3dcx__assembly_1__model_1

3dcx__assembly_1__model_1 | I(q)

3dcx__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) 11 domains

SCOP 2.08 (6 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Crystal structure of a duf1696 family protein with a pleckstrin-homology domain (shew_0819) from shewanella loihica pv-4 at 2.00 A resolution

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

Protein of Unknown Function (DUF1696) with Pleckstrin-homology Domains

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

3dcx__assembly_1__model_1

3dcx__assembly_1__model_1 | I(q)

3dcx__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) 11 domains

SCOP 2.08 (6 domains)

CATH v4.4 (5 domains)

7. Citations (1)