SAXSdb — 3db7

▼

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

putative calcium-regulated periplasmic protein

Bacteroides thetaiotaomicron

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 6 1,2-ETHANEDIOL × 4 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 3 1,2-ETHANEDIOL × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8A994_BACTN
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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3db7
Deposition date deposition_date	2008-05-30
Structure title title	Crystal structure of a putative calcium-regulated periplasmic protein (bt0923) from bacteroides thetaiotaomicron at 1.40 A resolution
Keywords keywords	Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, ca-binding protein; Ca-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.

3db7__assembly_2__model_1

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

Download this curve (.dat)

3db7__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3db7__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	16.09 Å
Rg (electron density)	15.09 Å
Total Rg	16.11 Å
Atom count	1024
Residues	125
Excluded volume	18444 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3db7__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3db7__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	putative calcium-regulated periplasmic protein
Molecular weight formula_weight	14790.5 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	1304

GADDDKPIQVTQMPQLAQQFIKQHFSDSKVALAKMESDFLYKSYEVIFTNGNKVEFDKKGNWEEVDCKHTSVPVAIIPAAIQKYVTTNYPDAKVLKIERDKKDYEVKLSNRTELKFDLKFNLIDIDN

Source Source

Source organism organism	Bacteroides thetaiotaomicron
NCBI taxonomy ID ncbi_taxonomy_id	818
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	194

▼

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3db7a1
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	d3db7a2
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	3db7A00
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 —

▶

Unit-cell length a length_a	66.170 Å
Unit-cell length b length_b	48.420 Å
Unit-cell length c length_c	44.610 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.27 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	24.922 Å
R factor r_factor	0.1623
R_work r_work	0.1603
R_free r_free	0.1982

Crystal structure of a putative calcium-regulated periplasmic protein (bt0923) from bacteroides thetaiotaomicron at 1.40 A resolution

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

putative calcium-regulated 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

3db7__assembly_2__model_1

3db7__assembly_2__model_1 | I(q)

3db7__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 (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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of a putative calcium-regulated periplasmic protein (bt0923) from bacteroides thetaiotaomicron at 1.40 A resolution

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

putative calcium-regulated 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

3db7__assembly_2__model_1

3db7__assembly_2__model_1 | I(q)

3db7__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 (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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)