SAXSdb — 3kbl

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

Female germline-specific tumor suppressor gld-1

Caenorhabditis elegans

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
2	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	GLD1_CAEEL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–60； UniProt 144–200 Author chain B； PDBConstruct 4–60； UniProt 144–200 Author chain C； PDBConstruct 4–60； UniProt 144–200 Author chain D； PDBConstruct 4–60； UniProt 144–200

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	3kbl
Deposition date deposition_date	2009-10-20
Structure title title	Crystal structure of the GLD-1 homodimerization domain from Caenorhabditis elegans N169A mutant at 2.28 A resolution
Keywords keywords	;GLD-1, N169A MUTANT, QUA1 HOMODIMERIZATION DOMAIN, HELIX-TURN-HELIX MOTIF, HYDROPHOBIC HOMODIMER INTERFACE, PERPENDICULAR STACKING OF PROTOMERS, Developmental protein, Differentiation, Meiosis, Oogenesis, RNA-binding, Translation regulation, PROTEIN BINDING ;; PROTEIN BINDING
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.

3kbl__assembly_2__model_1

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

Download this curve (.dat)

3kbl__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3kbl__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	15.72 Å
Rg (electron density)	14.99 Å
Total Rg	16.03 Å
Atom count	823
Residues	100
Excluded volume	14781 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3kbl__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3kbl__assembly_2__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 (2)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3kblA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4010 —

Domain ID domain_id	3kblB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4010 —

Domain ID domain_id	3kblC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4010 —

Domain ID domain_id	3kblD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4010 —

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Unit-cell length a length_a	34.406 Å
Unit-cell length b length_b	42.300 Å
Unit-cell length c length_c	156.144 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	16

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

Resolution resolution	2.280 Å
Low-resolution limit resolution_low	37.192 Å
R factor r_factor	0.1990
R_work r_work	0.1950
R_free r_free	0.2640

Description description	Female germline-specific tumor suppressor gld-1
Molecular weight formula_weight	6843.8 kDa
Mutation mutation	N169A
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	1684

Crystal structure of the GLD-1 homodimerization domain from Caenorhabditis elegans N169A mutant at 2.28 A resolution

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

Female germline-specific tumor suppressor gld-1

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

3kbl__assembly_2__model_1

3kbl__assembly_2__model_1 | I(q)

3kbl__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Caenorhabditis elegans
Common name common_name	nematode
NCBI taxonomy ID ncbi_taxonomy_id	6239
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	38

Crystal structure of the GLD-1 homodimerization domain from Caenorhabditis elegans N169A mutant at 2.28 A resolution

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

Female germline-specific tumor suppressor gld-1

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

3kbl__assembly_2__model_1

3kbl__assembly_2__model_1 | I(q)

3kbl__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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

CATH v4.4 (4 domains)

7. Citations (1)