SAXSdb — 1zgj

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

;Isoflavanone 4'-O-methyltransferase' ;

Medicago truncatula

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	(6AR,12AR)-3-(HYDROXYMETHYL)-6H-[1,3]DIOXOLO[5,6][1]BENZOFURO[3,2-C]CHROMEN-6A(12AH)-OL × 2 S-ADENOSYL-L-HOMOCYSTEINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q29U70_MEDTR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–354； UniProt 11–364

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	1zgj
Deposition date deposition_date	2005-04-21
Structure title title	Crystal structure of isoflavanone 4'-O-methyltransferase complexed with (+)-pisatin
Keywords keywords	;Rossma fold, Isoflavanone 4'-O-methyltransferase, Plant Protein, Transferase ;; Plant Protein, 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.

1zgj__assembly_1__model_1

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

Download this curve (.dat)

1zgj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zgj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.37 Å
Rg (electron density)	29.49 Å
Total Rg	30.05 Å
Atom count	5688
Residues	708
Excluded volume	101810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zgj__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	;Isoflavanone 4'-O-methyltransferase' ;
Molecular weight formula_weight	39750.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2867

SELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLSELASSLKLHPSKVNILHRFLRLLTHNGFFAKTIVKGKEGDEEEEIAYSLTPPSKLLISGKPTCLSSIVKGALHPSSLDMWSSSKKWFNEDKEQTLFECATGESFWDFLNKDSESSTLSMFQDAMASDSRMFKLVLQENKRVFEGLESLVDVGGGTGGVTKLIHEIFPHLKCTVFDQPQVVGNLTGNENLNFVGGDMFKSIPSADAVLLKWVLHDWNDEQSLKILKNSKEAISHKGKDGKVIIIDISIDETSDDRGLTELQLDYDLVMLTMFLGKERTKQEWEKLIYDAGFSSYKITPISGFKSLIEVYP

Source Source

Source organism organism	Medicago truncatula
Common name common_name	barrel medic
NCBI taxonomy ID ncbi_taxonomy_id	3880
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	(6AR,12AR)-3-(HYDROXYMETHYL)-6H-[1,3]DIOXOLO[5,6][1]BENZOFURO[3,2-C]CHROMEN-6A(12AH)-OL
Molecular weight formula_weight	314.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	23

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1zgja1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.0 — automated matches

Domain ID domain_id	d1zgja2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	1zgjA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1zgjA02
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

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Unit-cell length a length_a	71.786 Å
Unit-cell length b length_b	71.786 Å
Unit-cell length c length_c	188.697 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	8

Space group space_group	P 43 2 2
Space-group number int_tables_number	95
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	39.500 Å
R factor r_factor	0.2340
R_work r_work	0.2340
R_free r_free	0.2780

Crystal structure of isoflavanone 4'-O-methyltransferase complexed with (+)-pisatin

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

;Isoflavanone 4'-O-methyltransferase' ;

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

1zgj__assembly_1__model_1

1zgj__assembly_1__model_1 | I(q)

1zgj__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

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of isoflavanone 4'-O-methyltransferase complexed with (+)-pisatin

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

;Isoflavanone 4'-O-methyltransferase' ;

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

1zgj__assembly_1__model_1

1zgj__assembly_1__model_1 | I(q)

1zgj__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

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)