SAXSdb — 9j56

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

Aclacinomycin 10-hydroxylase RdmB

Streptomyces purpurascens

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 ;(7~{S},9~{S})-7-[(2~{R},4~{S},5~{S},6~{S})-4-azanyl-6-methyl-5-oxidanyl-oxan-2-yl]oxy-9-ethyl-4-methoxy-6,9,11-tris(oxidanyl)-8,10-dihydro-7~{H}-tetracene-5,12-dione ; × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

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

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	9j56
Deposition date deposition_date	2024-08-11
Last revision last_revision	2024-11-06
Structure title title	Functional Investigation of the SAM-Dependent Methyltransferases Rdmb in Anthracycline Biosynthesis
Keywords keywords	Methyltransferase domain-containing protein, RdmB, 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.

9j56__assembly_1__model_1

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

Download this curve (.dat)

9j56__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9j56__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.71 Å
Rg (electron density)	29.11 Å
Total Rg	29.58 Å
Atom count	5038
Residues	666
Excluded volume	89721 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9j56__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	Aclacinomycin 10-hydroxylase RdmB
Molecular weight formula_weight	39837.9 kDa
EC 编号 ec_number	4.1.1.-
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	5270

MSSSSPGEPLEPTDQDLDVLLKNLGNLVTPMALRVAATLRLVDHLLAGADTLAGLADRTDTHPQALSRLVRHLTVVGVLEGGEKQGRPLRPTRLGMLLADGHPAQQRAWLDLNGAVSHADLAFTGLLDVVRTGRPAYAGRYGRPFWEDLSADVALADSFDALMSCDEDLAYEAPADAYDWSAVRHVLDVGGGNGGMLAAIALRAPHLRGTLVELAGPAERARRRFADAGLADRVTVAEGDFFKPLPVTADVVLLSFVLLNWSDEDALTILRGCVRALEPGGRLLVLDRADVEGDGADRFFSTLLDLRMLTFMGGRVRTRDEVVDLAGSAGLALASERTSGSTTLPFDFSILEFTAVSEEAAPAAQASEALPAQE

Source Source

Source organism organism	Streptomyces purpurascens
NCBI taxonomy ID ncbi_taxonomy_id	1924
Host organism host_organism	Escherichia coli

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	;(7~{S},9~{S})-7-[(2~{R},4~{S},5~{S},6~{S})-4-azanyl-6-methyl-5-oxidanyl-oxan-2-yl]oxy-9-ethyl-4-methoxy-6,9,11-tris(oxidanyl)-8,10-dihydro-7~{H}-tetracene-5,12-dione ;
Molecular weight formula_weight	513.5 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	229

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Unit-cell length a length_a	79.997 Å
Unit-cell length b length_b	79.997 Å
Unit-cell length c length_c	234.203 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	44.719 Å
R factor r_factor	—
R_work r_work	0.2140
R_free r_free	0.2588

Functional Investigation of the SAM-Dependent Methyltransferases Rdmb in Anthracycline Biosynthesis

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

Aclacinomycin 10-hydroxylase RdmB

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

9j56__assembly_1__model_1

9j56__assembly_1__model_1 | I(q)

9j56__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

7. Citations (1)

Functional Investigation of the SAM-Dependent Methyltransferases Rdmb in Anthracycline Biosynthesis

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

Aclacinomycin 10-hydroxylase RdmB

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

9j56__assembly_1__model_1

9j56__assembly_1__model_1 | I(q)

9j56__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

7. Citations (1)