SAXSdb — 1vmk

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

purine nucleoside phosphorylase

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	GUANINE × 3 MAGNESIUM ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9X1T2_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–277； UniProt 1–265 Author chain B； PDBConstruct 13–277； UniProt 1–265 Author chain C； PDBConstruct 13–277； UniProt 1–265

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	1vmk
Deposition date deposition_date	2004-09-30
Structure title title	Crystal structure of Purine nucleoside phosphorylase (TM1596) from Thermotoga maritima at 2.01 A resolution
Keywords keywords	;TM1596, PURINE NUCLEOSIDE PHOSPHORYLASE, STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, Joint Center for Structural Genomics, 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.

1vmk__assembly_1__model_1

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

Download this curve (.dat)

1vmk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vmk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.72 Å
Rg (electron density)	27.69 Å
Total Rg	28.51 Å
Atom count	5625
Residues	740
Excluded volume	101670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vmk__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 (4)

Entity 1 Entity 1 polymer

Description description	purine nucleoside phosphorylase
Molecular weight formula_weight	30672.7 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	5969

MGSDKIHHHHHHMMKKIEEARTFISERTNLSPDILIILGSGFGPFIEKVEDPVIIDYKDIPHFPQPTVEGHSGKLVFGRISDKPVMIMAGRFHLYEGHDPATVAFPVYLAKYVGVKGVVVTNAAGAINPEFKPGEIILVRDIINFMFRNPLRGPNDEKIGPRFPDMSSVVDPEWARKIQERLSLKEGVYIGVLGPSYETPAEIRVFEKLGADLVGMSTVPEVIAAKHCGLKVVVFSCVTNMAAGITHGRLSHEEVVRTTKMAQGKIEKALTTAVEVF

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GUANINE
Molecular weight formula_weight	151.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	338

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1vmka_
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.56.2.1 — Purine and uridine phosphorylases

Domain ID domain_id	d1vmkb_
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.56.2.1 — Purine and uridine phosphorylases

Domain ID domain_id	d1vmkc_
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.56.2.1 — Purine and uridine phosphorylases

CATH v4.4 (3 domains)

Domain ID domain_id	1vmkA00
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	1vmkB00
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	1vmkC00
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	46.478 Å
Unit-cell length b length_b	74.601 Å
Unit-cell length c length_c	74.591 Å
Unit-cell angle α angle_alpha	117.34 °
Unit-cell angle β angle_beta	100.95 °
Unit-cell angle γ angle_gamma	100.71 °
Molecules per unit cell Z z_pdb	3

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

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	43.340 Å
R factor r_factor	0.2057
R_work r_work	0.2039
R_free r_free	0.2399

Crystal structure of Purine nucleoside phosphorylase (TM1596) from Thermotoga maritima at 2.01 A resolution

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

1vmk__assembly_1__model_1

1vmk__assembly_1__model_1 | I(q)

1vmk__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of Purine nucleoside phosphorylase (TM1596) from Thermotoga maritima at 2.01 A resolution

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

1vmk__assembly_1__model_1

1vmk__assembly_1__model_1 | I(q)

1vmk__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)