SAXSdb — 3b5i

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

S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase-like protein

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	S-ADENOSYL-L-HOMOCYSTEINE × 2 MAGNESIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9FLN8_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–374； UniProt 13–386 Author chain B； PDBConstruct 1–374； UniProt 13–386

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	3b5i
Deposition date deposition_date	2007-10-26
Structure title title	Crystal structure of Indole-3-acetic Acid Methyltransferase
Keywords keywords	methyltransferase, SABATH family, Indole-3-acetic acid, S-adenosyl-L-methionine, TRANSFERASE; TRANSFERASE
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.

3b5i__assembly_1__model_1

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

Download this curve (.dat)

3b5i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3b5i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.34 Å
Rg (electron density)	29.11 Å
Total Rg	29.95 Å
Atom count	5332
Residues	684
Excluded volume	94030 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3b5i__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase-like protein
Molecular weight formula_weight	40911.1 kDa
Mutation mutation	Q35L
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	5468

MKLERLLSMKGGKGQDSYANNSLAQAMHARSMLHLLEETLENVHLNSSASPPPFTAVDLGCSSGANTVHIIDFIVKHISKRFDAAGIDPPEFTAFFSDLPSNDFNTLFQLLPPLVSNTCMEECLAADGNRSYFVAGVPGSFYRRLFPARTIDFFHSAFSLHWLSQVPESVTDRRSAAYNRGRVFIHGAGEKTTTAYKRQFQADLAEFLRARAAEVKRGGAMFLVCLGRTSVDPTDQGGAGLLFGTHFQDAWDDLVREGLVAAEKRDGFNIPVYAPSLQDFKEVVDANGSFAIDKLVVYKGGSPLVVNEPDDASEVGRAFASSCRSVAGVLVEAHIGEELSNKLFSRVESRATSHAKDVLVNLQFFHIVASLSFT

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(DE3)

Entity 2 Entity 2 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	136

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3b5iA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	3b5iA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	220 —

Domain ID domain_id	3b5iB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	3b5iB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	220 —

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Unit-cell length a length_a	67.270 Å
Unit-cell length b length_b	129.400 Å
Unit-cell length c length_c	68.330 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.30 °
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	2.750 Å
Low-resolution limit resolution_low	45.220 Å
R factor r_factor	0.2580
R_work r_work	0.2570
R_free r_free	0.2820

Crystal structure of Indole-3-acetic Acid Methyltransferase

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

S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase-like protein

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

3b5i__assembly_1__model_1

3b5i__assembly_1__model_1 | I(q)

3b5i__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Indole-3-acetic Acid Methyltransferase

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

S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase-like protein

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

3b5i__assembly_1__model_1

3b5i__assembly_1__model_1 | I(q)

3b5i__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)