SAXSdb — 2dr3

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

UPF0273 protein PH0284

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	ADENOSINE-5'-DIPHOSPHATE × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y284_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–247； UniProt 1–247 Author chain B； PDBConstruct 1–247； UniProt 1–247 Author chain C； PDBConstruct 1–247； UniProt 1–247 Author chain D； PDBConstruct 1–247； UniProt 1–247 Author chain E； PDBConstruct 1–247； UniProt 1–247 Author chain F； PDBConstruct 1–247； UniProt 1–247

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	2dr3
Deposition date deposition_date	2006-06-06
Structure title title	Crystal Structure of RecA superfamily ATPase PH0284 from Pyrococcus horikoshii OT3
Keywords keywords	;RecA superfamily ATPase, Hexamer, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

2dr3__assembly_1__model_1

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

Download this curve (.dat)

2dr3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dr3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.49 Å
Rg (electron density)	35.53 Å
Total Rg	36.12 Å
Atom count	11301
Residues	1419
Excluded volume	202270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dr3__assembly_1__model_1`	hexameric （6）	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	UPF0273 protein PH0284
Molecular weight formula_weight	27571.0 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	12543

MTRRVKTGIPGVDEILHGGIPERNVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVALEEHPVQVRQNMAQFGWDVKPYEEKGMFAMVDAFTAGIGKSKEYEKYIVHDLTDIREFIEVLRQAIRDINAKRVVVDSVTTLYINKPAMARSIILQLKRVLAGTGCTSIFVSQVSVGERGFGGPGVEHGVDGIIRLDLDEIDGELKRSLIVWKMRGTSHSMRRHPFDITDKGIIVYPDKVLKRGKVLEL

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1242

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2dr3A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2dr3B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2dr3C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2dr3D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2dr3E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2dr3F00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	96.057 Å
Unit-cell length b length_b	96.057 Å
Unit-cell length c length_c	298.897 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	36

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	38.380 Å
R factor r_factor	0.2510
R_work r_work	0.2510
R_free r_free	0.2950

Crystal Structure of RecA superfamily ATPase PH0284 from Pyrococcus horikoshii OT3

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

UPF0273 protein PH0284

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

2dr3__assembly_1__model_1

2dr3__assembly_1__model_1 | I(q)

2dr3__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 (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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of RecA superfamily ATPase PH0284 from Pyrococcus horikoshii OT3

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

UPF0273 protein PH0284

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

2dr3__assembly_1__model_1

2dr3__assembly_1__model_1 | I(q)

2dr3__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 (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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)