SAXSdb — 2dvn

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

Hypothetical protein PH1917

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 13 INOSINIC ACID × 2 GLYCEROL × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O59580_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–186； UniProt 1–186 Author chain B； PDBConstruct 1–186； UniProt 1–186

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	2dvn
Deposition date deposition_date	2006-07-31
Structure title title	Structure of PH1917 protein with the complex of IMP from Pyrococcus horikoshii
Keywords keywords	;IMP, NTPase, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, HYDROLASE ;; 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.

2dvn__assembly_1__model_1

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

Download this curve (.dat)

2dvn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dvn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.94 Å
Rg (electron density)	21.96 Å
Total Rg	22.88 Å
Atom count	3135
Residues	372
Excluded volume	55962 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dvn__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	Hypothetical protein PH1917
Molecular weight formula_weight	21233.4 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	3560

MKIFFITSNPGKVREVANFLGTFGIEIVQLKHEYPEIQAEKLEDVVDFGISWLKGKVPEPFMIEDSGLFIESLKGFPGVYSSYVYRTIGLEGILKLMEGAEDRRAYFKSVIGFYIDGKAYKFSGVTWGRISNEKRGTHGFGYDPIFIPEGSEKTFAEMTIEEKNALSHRGKALKAFFEWLKVNLKY

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	53953
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 3 Entity 3 non-polymer

Description description	INOSINIC ACID
Molecular weight formula_weight	348.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	425

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2dvna_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.4 — ITPase-like
Family Family family	c.51.4.1 — ITPase (Ham1)

Domain ID domain_id	d2dvnb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.4 — ITPase-like
Family Family family	c.51.4.1 — ITPase (Ham1)

CATH v4.4 (2 domains)

Domain ID domain_id	2dvnA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	950 — Maf protein
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2dvnB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	950 — Maf protein
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	80.295 Å
Unit-cell length b length_b	80.295 Å
Unit-cell length c length_c	162.367 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	39.180 Å
R factor r_factor	0.1830
R_work r_work	0.1830
R_free r_free	0.1880

Structure of PH1917 protein with the complex of IMP from Pyrococcus horikoshii

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

Hypothetical protein PH1917

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

2dvn__assembly_1__model_1

2dvn__assembly_1__model_1 | I(q)

2dvn__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of PH1917 protein with the complex of IMP from Pyrococcus horikoshii

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

Hypothetical protein PH1917

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

2dvn__assembly_1__model_1

2dvn__assembly_1__model_1 | I(q)

2dvn__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)