SAXSdb — 4o30

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

Histone-lysine N-methyltransferase ATXR6, putative

Ricinus communis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	histone H3.1 × 1 S-ADENOSYL-L-HOMOCYSTEINE × 1 DIMETHYL SULFOXIDE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	histone H3.1 × 1 S-ADENOSYL-L-HOMOCYSTEINE × 1 BETA-MERCAPTOETHANOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B9RU15_RICCO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–234； UniProt 146–374 Author chain B； PDBConstruct 6–234； UniProt 146–374

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	4o30
Deposition date deposition_date	2013-12-17
Structure title title	Crystal structure of ATXR5 in complex with histone H3.1 and AdoHcy
Keywords keywords	;histone methylation, chromatin, epigenetics, trithorax, SET domain, lysine methyltransferases, PCNA, histone H3, nucleus, 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.

4o30__assembly_1__model_1

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

Download this curve (.dat)

4o30__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4o30__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.89 Å
Rg (electron density)	16.70 Å
Total Rg	17.65 Å
Atom count	1813
Residues	231
Excluded volume	31887 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4o30__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4o30__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 (6)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase ATXR6, putative
Molecular weight formula_weight	26650.3 kDa
EC 编号 ec_number	2.1.1.43
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	3911

GAMGSRRRSGSLVYQKRRRRLLPFVSSEDPAQRLKQMGTLASALTELQMEFSDDLTYSSGMAPRSANQARFEEGGMQVLTKEDIETLEQCRAMCKRGDCPPLLVVFDSREGFTVEADGQIKDMTFIAEYTGDVDYIRNREHDDCDSMMTLLLAKDPSKSLVICPDKRGNIARFISGINNHTLDGKKKQNCKCVRYSVNGECRVFLVATRDIAKGERLYYDYNGYEHEYPTQHFV

Source Source

Source organism organism	Ricinus communis
Common name common_name	Castor bean
NCBI taxonomy ID ncbi_taxonomy_id	3988
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	histone H3.1
Molecular weight formula_weight	1888.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

KQLATKAARKSAPATGGVK

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	2

Entity 4 Entity 4 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	302

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4o30A00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

Domain ID domain_id	4o30B00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

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Unit-cell length a length_a	101.170 Å
Unit-cell length b length_b	87.310 Å
Unit-cell length c length_c	74.510 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	127.78 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	27.000 Å
R factor r_factor	0.2042
R_work r_work	0.2019
R_free r_free	0.2472

Crystal structure of ATXR5 in complex with histone H3.1 and AdoHcy

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

Histone-lysine N-methyltransferase ATXR6, putative

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

4o30__assembly_1__model_1

4o30__assembly_1__model_1 | I(q)

4o30__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 polymer

Polymer 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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of ATXR5 in complex with histone H3.1 and AdoHcy

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

Histone-lysine N-methyltransferase ATXR6, putative

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

4o30__assembly_1__model_1

4o30__assembly_1__model_1 | I(q)

4o30__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 polymer

Polymer 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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)