SAXSdb — 2ynq

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

ESSB

GEOBACILLUS THERMODENITRIFICANS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MALONATE ION × 1 SODIUM ION × 3 CHLORIDE ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MALONATE ION × 2 SODIUM ION × 2 CHLORIDE ION × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	MALONATE ION × 2 SODIUM ION × 2 CHLORIDE ION × 2 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	MALONATE ION × 2 SODIUM ION × 3 CHLORIDE ION × 2 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	MALONATE ION × 1 SODIUM ION × 2 CHLORIDE ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4IKE6_GEOTN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–161； UniProt 241–397 Author chain B； PDBConstruct 5–160； UniProt 241–397 Author chain C； PDBConstruct 5–161； UniProt 241–397 Author chain D； PDBConstruct 5–161； UniProt 241–397

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	2ynq
Deposition date deposition_date	2012-10-17
Structure title title	Crystal Structure of Geobacillus thermodenitrificans EssB extracellular fragment
Keywords keywords	MEMBRANE PROTEIN, SECRETION, ESS, TYPE V, SECRETION SYSTEM; MEMBRANE PROTEIN
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.

2ynq__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ynq__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ynq__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	24.76 Å
Rg (electron density)	23.78 Å
Total Rg	24.56 Å
Atom count	2501
Residues	298
Excluded volume	44196 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ynq__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ynq__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2ynq__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2ynq__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2ynq__assembly_5__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 (6)

Entity 1 Entity 1 polymer

Description description	ESSB
Molecular weight formula_weight	18992.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5452

GASTAQPKQEAYIQSTELFLQNKYSDVITTLEDYAPEDMPYVIQYELASSYVMTESLTEEQRQTVSNNITLKTDEQYMLYWIYIGRSQSEEALELARTIEDRDLIVYALLKYREQIKGDTDLSGDEKQKKLDEIDQEIKEYERERKESEAQLEEEQQSEQQ

Source Source

Source organism organism	GEOBACILLUS THERMODENITRIFICANS
NCBI taxonomy ID ncbi_taxonomy_id	420246
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	246

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2ynqA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	680 — Type VII secretion system EssB, C-terminal-like domain

Domain ID domain_id	2ynqB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	680 — Type VII secretion system EssB, C-terminal-like domain

Domain ID domain_id	2ynqC00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	680 — Type VII secretion system EssB, C-terminal-like domain

Domain ID domain_id	2ynqD00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	680 — Type VII secretion system EssB, C-terminal-like domain

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Unit-cell length a length_a	132.890 Å
Unit-cell length b length_b	110.620 Å
Unit-cell length c length_c	97.410 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.34 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	94.782 Å
R factor r_factor	0.1880
R_work r_work	0.1862
R_free r_free	0.2215

Crystal Structure of Geobacillus thermodenitrificans EssB extracellular fragment

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

ESSB

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

2ynq__assembly_3__model_1

2ynq__assembly_3__model_1 | I(q)

2ynq__assembly_3__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Geobacillus thermodenitrificans EssB extracellular fragment

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

ESSB

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

2ynq__assembly_3__model_1

2ynq__assembly_3__model_1 | I(q)

2ynq__assembly_3__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)