SAXSdb — 1xdu

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

Protein RdmB

Streptomyces purpurascens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ACETATE ION × 1 SINEFUNGIN × 1 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ACETATE ION × 2 SINEFUNGIN × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q54527_9ACTO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； 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	1xdu
Deposition date deposition_date	2004-09-08
Structure title title	Crystal structure of Aclacinomycin-10-hydroxylase (RdmB) in complex with Sinefungin (SFG)
Keywords keywords	;Anthracycline; hydroxylase; S-adenosyl-L-methionine analogue; sinefungin; streptomyces; polyketide antibiotics; divergent evolution, 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.

1xdu__assembly_1__model_1

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

Download this curve (.dat)

1xdu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xdu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.03 Å
Rg (electron density)	23.30 Å
Total Rg	24.02 Å
Atom count	2601
Residues	334
Excluded volume	46224 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xdu__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1xdu__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 (4)

Entity 1 Entity 1 polymer

Description description	Protein RdmB
Molecular weight formula_weight	40166.2 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	2627

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	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SINEFUNGIN
Molecular weight formula_weight	381.4 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	26

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1xdua1
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.4.5.29 — Plant O-methyltransferase, N-terminal domain

Domain ID domain_id	d1xdua2
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.66.1.12 — Plant O-methyltransferase, C-terminal domain

CATH v4.4 (3 domains)

Domain ID domain_id	1xduA01
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	1xduA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1350 —

Domain ID domain_id	1xduA03
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	62.758 Å
Unit-cell length b length_b	86.813 Å
Unit-cell length c length_c	117.395 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	58.720 Å
R factor r_factor	0.2306
R_work r_work	0.2274
R_free r_free	0.2951

Crystal structure of Aclacinomycin-10-hydroxylase (RdmB) in complex with Sinefungin (SFG)

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

Protein 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

1xdu__assembly_1__model_1

1xdu__assembly_1__model_1 | I(q)

1xdu__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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of Aclacinomycin-10-hydroxylase (RdmB) in complex with Sinefungin (SFG)

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

Protein 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

1xdu__assembly_1__model_1

1xdu__assembly_1__model_1 | I(q)

1xdu__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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)