SAXSdb — 1sbk

▼

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

Hypothetical protein ydiI

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YDII_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–136； UniProt 1–136 Author chain B； PDBConstruct 1–136； UniProt 1–136 Author chain C； PDBConstruct 1–136； UniProt 1–136 Author chain D； PDBConstruct 1–136； UniProt 1–136

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	1sbk
Deposition date deposition_date	2004-02-10
Structure title title	X-RAY STRUCTURE OF YDII_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER29.
Keywords keywords	;er29, YDII, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

1sbk__assembly_1__model_1

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

Download this curve (.dat)

1sbk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1sbk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.77 Å
Rg (electron density)	22.74 Å
Total Rg	23.65 Å
Atom count	4268
Residues	536
Excluded volume	76041 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1sbk__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Hypothetical protein ydiI
Molecular weight formula_weight	16225.0 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	4693

MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAILLEHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	425

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1sbka1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.5 — PaaI/YdiI-like

Domain ID domain_id	d1sbka2
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	d1sbkb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.5 — PaaI/YdiI-like

Domain ID domain_id	d1sbkb2
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	d1sbkc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.5 — PaaI/YdiI-like

Domain ID domain_id	d1sbkc2
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	d1sbkd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.5 — PaaI/YdiI-like

Domain ID domain_id	d1sbkd2
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 (4 domains)

Domain ID domain_id	1sbkA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	1sbkB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	1sbkC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	1sbkD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

▶

Unit-cell length a length_a	46.642 Å
Unit-cell length b length_b	61.196 Å
Unit-cell length c length_c	93.008 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.66 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	28.970 Å
R factor r_factor	0.2230
R_work r_work	0.2230
R_free r_free	0.2720

X-RAY STRUCTURE OF YDII_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER29.

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

Hypothetical protein ydiI

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

1sbk__assembly_1__model_1

1sbk__assembly_1__model_1 | I(q)

1sbk__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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

X-RAY STRUCTURE OF YDII_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER29.

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

Hypothetical protein ydiI

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

1sbk__assembly_1__model_1

1sbk__assembly_1__model_1 | I(q)

1sbk__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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)