2wbm

Crystal structure of mthSBDS, the homologue of the Shwachman-Bodian- Diamond syndrome protein in the euriarchaeon Methanothermobacter thermautotrophicus

Method: X-RAY DIFFRACTION

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

RIBOSOME MATURATION PROTEIN SDO1 HOMOLOG

METHANOTHERMOBACTER THERMAUTOTROPHICUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	GLYCEROL × 4 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	GLYCEROL × 2 SULFATE ION × 3 CHLORIDE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SDO1_METTH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–252； UniProt 1–232 Author chain B； PDBConstruct 21–252； UniProt 1–232

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	2wbm
Deposition date deposition_date	2009-03-02
Structure title title	Crystal structure of mthSBDS, the homologue of the Shwachman-Bodian- Diamond syndrome protein in the euriarchaeon Methanothermobacter thermautotrophicus
Keywords keywords	SHWACHMAN-BODIAN-DIAMOND SYNDROME PROTEIN, RIBOSOME BINDING, CONFORMATIONAL FLEXIBILITY, RNA-BINDING PROTEIN, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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.

2wbm__assembly_1__model_1

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

Download this curve (.dat)

2wbm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wbm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.90 Å
Rg (electron density)	24.22 Å
Total Rg	24.83 Å
Atom count	1881
Residues	234
Excluded volume	33563 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wbm__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2wbm__assembly_2__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	RIBOSOME MATURATION PROTEIN SDO1 HOMOLOG
Molecular weight formula_weight	28377.4 kDa
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	4230

MGSSHHHHHHSSGLVPRGSHMVSLEDAVIARLESHGERFEVLVDPDLAAEFRREDSDVSVEDVLAVQEVFRDARKGDKASEEAMRKVFETADPLEVTPVILRRGTIQLTAEQRRQMIEDKRLKIINKIAREAINPQNGLPHPPKRIEKAMEEARVHVDPFKTVDEQVNIVLKAIRTKIPIKFEKVRVAIKIPGEMAGSAYGVISNFGKITNEEWQNDGSWIAVVEIPGGLQDSFYQKLSELTGGNVETRLIK

Source Source

Source organism organism	METHANOTHERMOBACTER THERMAUTOTROPHICUS
NCBI taxonomy ID ncbi_taxonomy_id	187420
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	411

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d2wbma1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.235 — FYSH domain
Superfamily Superfamily superfamily	d.235.1 — FYSH domain
Family Family family	d.235.1.0 — automated matches

Domain ID domain_id	d2wbma2
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.8 — Hypothetical protein AF0491, middle domain
Family Family family	a.5.8.0 — automated matches

Domain ID domain_id	d2wbma3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.11 — EF-G C-terminal domain-like
Family Family family	d.58.11.0 — automated matches

Domain ID domain_id	d2wbma4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2wbmb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.235 — FYSH domain
Superfamily Superfamily superfamily	d.235.1 — FYSH domain
Family Family family	d.235.1.0 — automated matches

Domain ID domain_id	d2wbmb2
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.8 — Hypothetical protein AF0491, middle domain
Family Family family	a.5.8.0 — automated matches

Domain ID domain_id	d2wbmb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.11 — EF-G C-terminal domain-like
Family Family family	d.58.11.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	2wbmA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1250 — Hypothetical 12.0 Kda Protein In Nam8-gar1 Intergenic Region; Chain: A;
Homologous superfamily homologous superfamily	10 — Ribosome maturation protein SBDS, N-terminal domain

Domain ID domain_id	2wbmA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	900 — SBDS protein C-terminal domain, subdomain 1

Domain ID domain_id	2wbmA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	240 —

Domain ID domain_id	2wbmB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1250 — Hypothetical 12.0 Kda Protein In Nam8-gar1 Intergenic Region; Chain: A;
Homologous superfamily homologous superfamily	10 — Ribosome maturation protein SBDS, N-terminal domain

Domain ID domain_id	2wbmB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	900 — SBDS protein C-terminal domain, subdomain 1

Domain ID domain_id	2wbmB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	240 —

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Unit-cell length a length_a	68.300 Å
Unit-cell length b length_b	72.108 Å
Unit-cell length c length_c	146.829 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 2 2 21
Space-group number int_tables_number	17
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	26.980 Å
R factor r_factor	0.1910
R_work r_work	0.1910
R_free r_free	0.2140

Crystal structure of mthSBDS, the homologue of the Shwachman-Bodian- Diamond syndrome protein in the euriarchaeon Methanothermobacter thermautotrophicus

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

RIBOSOME MATURATION PROTEIN SDO1 HOMOLOG

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

2wbm__assembly_1__model_1

2wbm__assembly_1__model_1 | I(q)

2wbm__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of mthSBDS, the homologue of the Shwachman-Bodian- Diamond syndrome protein in the euriarchaeon Methanothermobacter thermautotrophicus

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

RIBOSOME MATURATION PROTEIN SDO1 HOMOLOG

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

2wbm__assembly_1__model_1

2wbm__assembly_1__model_1 | I(q)

2wbm__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

CATH v4.4 (6 domains)

7. Citations (1)