SAXSdb — 3f8w

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

Purine-nucleoside phosphorylase

Schistosoma mansoni

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	ADENOSINE × 3 SULFATE ION × 3 DIMETHYL SULFOXIDE × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9BMI9_SCHMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–287； UniProt 1–287 Author chain B； PDBConstruct 1–287； UniProt 1–287 Author chain C； PDBConstruct 1–287； UniProt 1–287

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	3f8w
Deposition date deposition_date	2008-11-13
Structure title title	Crystal structure of Schistosoma mansoni purine nucleoside phosphorylase in complex with adenosine
Keywords keywords	Purine Nucleoside Phosphorylase, Schistosoma, adenosine, Glycosyltransferase, 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.

3f8w__assembly_1__model_1

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

Download this curve (.dat)

3f8w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3f8w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.69 Å
Rg (electron density)	28.04 Å
Total Rg	28.75 Å
Atom count	6462
Residues	843
Excluded volume	116120 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3f8w__assembly_1__model_1`	trimeric （3）	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	Purine-nucleoside phosphorylase
Molecular weight formula_weight	31197.3 kDa
EC 编号 ec_number	2.4.2.1
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6803

MHESVTANIENVKKVAHHIQKLTSIVPEIGIICGSGLGKLADGVKDKITIPYTKIPNFPQTSVVGHSGNLIFGTLSGRKVVVMQGRFHMYEGYSNDTVALPIRVMKLLGVKILMVSNAAGGLNRSLKLGDFVILKDHIYLPGLGLNNILVGPNQEAFGTRFPALSNAYDRDLRKLAVQVAEENGFGNLVHQGVYVMNGGPCYETPAECTMLLNMGCDVVGMSTIPEVVIARHCGIQVFAVSLVTNISVLDVESDLKPNHEEVLATGAQRAELMQSWFEKIIEKLPKD

Source Source

Source organism organism	Schistosoma mansoni
NCBI taxonomy ID ncbi_taxonomy_id	6183
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE
Molecular weight formula_weight	267.2 kDa
Source method src_method	syn
Copy count entity_count	3

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	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	334

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3f8wa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.0 — automated matches

Domain ID domain_id	d3f8wb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.0 — automated matches

Domain ID domain_id	d3f8wc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	3f8wA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

Domain ID domain_id	3f8wB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

Domain ID domain_id	3f8wC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

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Unit-cell length a length_a	49.715 Å
Unit-cell length b length_b	121.273 Å
Unit-cell length c length_c	133.248 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	46.009 Å
R factor r_factor	0.1760
R_work r_work	0.1740
R_free r_free	0.2040

Crystal structure of Schistosoma mansoni purine nucleoside phosphorylase in complex with adenosine

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

Purine-nucleoside phosphorylase

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

3f8w__assembly_1__model_1

3f8w__assembly_1__model_1 | I(q)

3f8w__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (2)

Crystal structure of Schistosoma mansoni purine nucleoside phosphorylase in complex with adenosine

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

Purine-nucleoside phosphorylase

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

3f8w__assembly_1__model_1

3f8w__assembly_1__model_1 | I(q)

3f8w__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (2)