SAXSdb — 3due

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

Putative periplasmic protein

Bacteroides vulgatus ATCC 8482

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A6L4L1_BACV8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–127； UniProt 20–145

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	3due
Deposition date deposition_date	2008-07-17
Structure title title	CRYSTAL STRUCTURE OF A PUTATIVE PERIPLASMIC PROTEIN FROM DUF2874 FAMILY (BVU_2987) FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.85 A RESOLUTION
Keywords keywords	;PUTATIVE PERIPLASMIC PROTEIN, 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.

3due__assembly_1__model_1

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

Download this curve (.dat)

3due__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3due__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.27 Å
Rg (electron density)	15.20 Å
Total Rg	16.16 Å
Atom count	1024
Residues	123
Excluded volume	18243 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3due__assembly_1__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	Putative periplasmic protein
Molecular weight formula_weight	14889.2 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	1183

GADDDKPIQVNQLPQTAQTFIKTHFPDNKVAMAKMETDWFDKSYDVIFTNGDKLEFDKKGIWTEVNCKYSAVPVAVVPDAIKKYVATNYPDAKMLKIERDKHDYEVKLSNGWEIKFDMQFNVIDIDN

Source Source

Source organism organism	Bacteroides vulgatus ATCC 8482
NCBI taxonomy ID ncbi_taxonomy_id	435590
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 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	133

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3duea1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.98 — BLIP-like
Superfamily Superfamily superfamily	d.98.2 — BT0923-like
Family Family family	d.98.2.1 — BT0923-like

Domain ID domain_id	d3duea2
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

CATH v4.4 (1 domains)

Domain ID domain_id	3dueA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1420 — Inhibitor of vertebrate lysozyme, Ivy
Homologous superfamily homologous superfamily	30 —

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Unit-cell length a length_a	31.601 Å
Unit-cell length b length_b	50.874 Å
Unit-cell length c length_c	79.507 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	4

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

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	29.361 Å
R factor r_factor	0.1943
R_work r_work	0.1923
R_free r_free	0.2332

CRYSTAL STRUCTURE OF A PUTATIVE PERIPLASMIC PROTEIN FROM DUF2874 FAMILY (BVU_2987) FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.85 A RESOLUTION

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

Putative periplasmic 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

3due__assembly_1__model_1

3due__assembly_1__model_1 | I(q)

3due__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF A PUTATIVE PERIPLASMIC PROTEIN FROM DUF2874 FAMILY (BVU_2987) FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.85 A RESOLUTION

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

Putative periplasmic 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

3due__assembly_1__model_1

3due__assembly_1__model_1 | I(q)

3due__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)