SAXSdb — 8z53

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

Strigolactone esterase D14

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(7E)-6-methyl-8-[(4S)-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octa-3,5,7-trien-2-one × 1 DI(HYDROXYETHYL)ETHER × 1 GLYCEROL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(7E)-6-methyl-8-[(4S)-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octa-3,5,7-trien-2-one × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D14_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–265； UniProt 2–266 Author chain B； PDBConstruct 1–265； UniProt 2–266

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	8z53
Deposition date deposition_date	2024-04-18
Structure title title	Arabidopsis Dwarf14 (AtD14) co-crystallized in the presence of Zaxinone
Keywords keywords	AtD14, Zaxinone, Strigolactone, HYDROLASE; HYDROLASE
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.

8z53__assembly_1__model_1

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

Download this curve (.dat)

8z53__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8z53__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.84 Å
Rg (electron density)	17.27 Å
Total Rg	18.33 Å
Atom count	2107
Residues	265
Excluded volume	37514 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8z53__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8z53__assembly_2__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	Strigolactone esterase D14
Molecular weight formula_weight	29365.3 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4238

SQHNILEALNVRVVGTGDRILFLAHGFGTDQSAWHLILPYFTQNYRVVLYDLVCAGSVNPDYFDFNRYTTLDPYVDDLLNIVDSLGIQNCAYVGHSVSAMIGIIASIRRPELFSKLILIGFSPRFLNDEDYHGGFEEGEIEKVFSAMEANYEAWVHGFAPLAVGADVPAAVREFSRTLFNMRPDISLFVSRTVFNSDLRGVLGLVRVPTCVIQTAKDVSVPASVAEYLRSHLGGDTTVETLKTEGHLPQLSAPAQLAQFLRRALP

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	thale cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	(7E)-6-methyl-8-[(4S)-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octa-3,5,7-trien-2-one
Molecular weight formula_weight	274.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	62

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Unit-cell length a length_a	43.820 Å
Unit-cell length b length_b	69.580 Å
Unit-cell length c length_c	89.860 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.85 °
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	2.400 Å
Low-resolution limit resolution_low	44.910 Å
R factor r_factor	0.1802
R_work r_work	0.1777
R_free r_free	0.2264

Arabidopsis Dwarf14 (AtD14) co-crystallized in the presence of Zaxinone

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

Strigolactone esterase D14

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

8z53__assembly_1__model_1

8z53__assembly_1__model_1 | I(q)

8z53__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 (5)

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 water

7. Citations (1)

Arabidopsis Dwarf14 (AtD14) co-crystallized in the presence of Zaxinone

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

Strigolactone esterase D14

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

8z53__assembly_1__model_1

8z53__assembly_1__model_1 | I(q)

8z53__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 (5)

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 water

7. Citations (1)