SAXSdb — 1w1b

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

PROBABLE POLYSACCHARIDE DEACETYLASE PDAA

BACILLUS SUBTILIS

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDAA_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 1； PDBConstruct 6–257； UniProt 12–263 Author chain 2； PDBConstruct 6–257； UniProt 12–263

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	1w1b
Deposition date deposition_date	2004-06-18
Structure title title	Structure of Bacillus subtilis PdaA with Cadmium, a family 4 Carbohydrate esterase.
Keywords keywords	FAMILY 4 CARBOHYDRATE ESTERASE, DEACETYLASE, PEPTIDOGLYCAN, NODB HOMOLOGY DOMAIN, HYDROLASE, SPORULATION; HYDROLASE
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.

1w1b__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1w1b__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1w1b__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	18.28 Å
Rg (electron density)	17.11 Å
Total Rg	18.23 Å
Atom count	1921
Residues	235
Excluded volume	34130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1w1b__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1w1b__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 (3)

Entity 1 Entity 1 polymer

Description description	PROBABLE POLYSACCHARIDE DEACETYLASE PDAA
Molecular weight formula_weight	29294.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,2
Atom count atom_count	4195

GPLGSVLLAGGAAQAEAVPNEPINWGFKRSVNHQPPDAGKQLNSLIEKYDAFYLGNTKEKTIYLTFDNGYENGYTPKVLDVLKKHRVTGTFFVTGHFVKDQPQLIKRMSDEGHIIGNHSFHHPDLTTKTADQIQDELDSVNEEVYKITGKQDNLYLRPPRGVFSEYVLKETKRLGYQTVFWSVAFVDWKINNQKGKKYAYDHMIKQAHPGAIYLLHTVSRDNAEALDDAITDLKKQGYTFKSIDDLMFEKEMRLPSL

Source Source

Source organism organism	BACILLUS SUBTILIS
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	345

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1w1b1_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.6 — 7-stranded beta/alpha barrel
Superfamily Superfamily superfamily	c.6.2 — Glycoside hydrolase/deacetylase
Family Family family	c.6.2.3 — NodB-like polysaccharide deacetylase

Domain ID domain_id	d1w1b2_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.6 — 7-stranded beta/alpha barrel
Superfamily Superfamily superfamily	c.6.2 — Glycoside hydrolase/deacetylase
Family Family family	c.6.2.3 — NodB-like polysaccharide deacetylase

CATH v4.4 (2 domains)

Domain ID domain_id	1w1b100
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	370 — Glycoside hydrolase/deacetylase

Domain ID domain_id	1w1b200
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	370 — Glycoside hydrolase/deacetylase

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Unit-cell length a length_a	87.824 Å
Unit-cell length b length_b	87.824 Å
Unit-cell length c length_c	120.562 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 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	24.850 Å
R factor r_factor	0.1790
R_work r_work	0.1790
R_free r_free	0.2270

Structure of Bacillus subtilis PdaA with Cadmium, a family 4 Carbohydrate esterase.

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

PROBABLE POLYSACCHARIDE DEACETYLASE PDAA

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

1w1b__assembly_2__model_1

1w1b__assembly_2__model_1 | I(q)

1w1b__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of Bacillus subtilis PdaA with Cadmium, a family 4 Carbohydrate esterase.

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

PROBABLE POLYSACCHARIDE DEACETYLASE PDAA

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

1w1b__assembly_2__model_1

1w1b__assembly_2__model_1 | I(q)

1w1b__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)