SAXSdb — 3ebl

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

Gibberellin receptor GID1

Oryza sativa subsp. japonica

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	GIBBERELLIN A4 × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 NITRATE ION × 4 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	GIBBERELLIN A4 × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 NITRATE ION × 3 PHOSPHATE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	GIBBERELLIN A4 × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 NITRATE ION × 4 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	GIBBERELLIN A4 × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 NITRATE ION × 3 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	GIBBERELLIN A4 × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 NITRATE ION × 1 PHOSPHATE ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	GIBBERELLIN A4 × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 NITRATE ION × 3 water × 1	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	GIBBERELLIN A4 × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 NITRATE ION × 4 PHOSPHATE ION × 1 water × 2	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 2	GIBBERELLIN A4 × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 NITRATE ION × 7 PHOSPHATE ION × 1 water × 2	Consistent with protein count
9	Protein homooligomer	Homooligomer	Protein 2	GIBBERELLIN A4 × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 NITRATE ION × 7 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GID1_ORYSJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–353； UniProt 2–354 Author chain B； PDBConstruct 1–353； UniProt 2–354 Author chain C； PDBConstruct 1–353； UniProt 2–354 Author chain D； PDBConstruct 1–353； UniProt 2–354 Author chain E； PDBConstruct 1–353； UniProt 2–354 Author chain F； PDBConstruct 1–353； UniProt 2–354

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	3ebl
Deposition date deposition_date	2008-08-28
Structure title title	Crystal Structure of Rice GID1 complexed with GA4
Keywords keywords	alpha/beta hydrolase, lipase, Gibberellin signaling pathway, Hydrolase, Nucleus, Receptor, HYDROLASE RECEPTOR; HYDROLASE RECEPTOR
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.

3ebl__assembly_1__model_1

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

Download this curve (.dat)

3ebl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ebl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.69 Å
Rg (electron density)	18.45 Å
Total Rg	19.40 Å
Atom count	2568
Residues	323
Excluded volume	45132 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ebl__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ebl__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3ebl__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3ebl__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3ebl__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3ebl__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3ebl__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3ebl__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`3ebl__assembly_9__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	Gibberellin receptor GID1
Molecular weight formula_weight	40900.7 kDa
EC 编号 ec_number	3.-.-.-
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	16004

AGSDEVNRNECKTVVPLHTWVLISNFKLSYNILRRADGTFERDLGEYLDRRVPANARPLEGVSSFDHIIDQSVGLEVRIYRAAAEGDAEEGAAAVTRPILEFLTDAPAAEPFPVIIFFHGGSFVHSSASSTIYDSLCRRFVKLSKGVVVSVNYRRAPEHRYPCAYDDGWTALKWVMSQPFMRSGGDAQARVFLSGDSSGGNIAHHVAVRAADEGVKVCGNILLNAMFGGTERTESERRLDGKYFVTLQDRDWYWKAYLPEDADRDHPACNPFGPNGRRLGGLPFAKSLIIVSGLDLTCDRQLAYADALREDGHHVKVVQCENATVGFYLLPNTVHYHEVMEEISDFLNANLYYGSHHHHHHHHHH

Source Source

Source organism organism	Oryza sativa subsp. japonica
Common name common_name	Rice
NCBI taxonomy ID ncbi_taxonomy_id	39947
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GIBBERELLIN A4
Molecular weight formula_weight	332.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1133

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3eblA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3eblB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3eblC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3eblD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3eblE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3eblF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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Unit-cell length a length_a	82.760 Å
Unit-cell length b length_b	133.895 Å
Unit-cell length c length_c	118.886 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.95 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2026
R_work r_work	0.2004
R_free r_free	0.2437

Crystal Structure of Rice GID1 complexed with GA4

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

Gibberellin receptor GID1

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

3ebl__assembly_1__model_1

3ebl__assembly_1__model_1 | I(q)

3ebl__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 (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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of Rice GID1 complexed with GA4

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

Gibberellin receptor GID1

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

3ebl__assembly_1__model_1

3ebl__assembly_1__model_1 | I(q)

3ebl__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 (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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)