SAXSdb — 1r8g

▼

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

Hypothetical protein ybdK

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAAL_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–372； UniProt 1–372 Author chain B； PDBConstruct 1–372； UniProt 1–372

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	1r8g
Deposition date deposition_date	2003-10-24
Structure title title	Structure and function of YbdK
Keywords keywords	;Structural Genomics, unknown function, YbdK, hypothetical protein, carboxylate-amine ligase, Structure 2 Function Project, S2F, LIGASE ;; LIGASE
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.

1r8g__assembly_1__model_1

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

Download this curve (.dat)

1r8g__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1r8g__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.76 Å
Rg (electron density)	26.85 Å
Total Rg	27.61 Å
Atom count	5578
Residues	690
Excluded volume	99167 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1r8g__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1r8ga_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.3 — Glutamate-cysteine ligase family 2 (GCS2)

Domain ID domain_id	d1r8gb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.3 — Glutamate-cysteine ligase family 2 (GCS2)

CATH v4.4 (2 domains)

Domain ID domain_id	1r8gA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1r8gB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily	20 —

▶

Unit-cell length a length_a	49.470 Å
Unit-cell length b length_b	100.320 Å
Unit-cell length c length_c	71.370 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.94 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1890
R_free r_free	0.2520

Description description	Hypothetical protein ybdK
Molecular weight formula_weight	42253.1 kDa
EC 编号 ec_number	6.3.-.-
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6234

Structure and function of YbdK

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

Hypothetical protein ybdK

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

1r8g__assembly_1__model_1

1r8g__assembly_1__model_1 | I(q)

1r8g__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	656

Structure and function of YbdK

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

Hypothetical protein ybdK

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

1r8g__assembly_1__model_1

1r8g__assembly_1__model_1 | I(q)

1r8g__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)