SAXSdb — 2ekd

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

Hypothetical protein PH0250

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	CHLORIDE ION × 3 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 12	CHLORIDE ION × 6 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O57988_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–207； UniProt 1–207 Author chain B； PDBConstruct 1–207； UniProt 1–207 Author chain C； PDBConstruct 1–207； UniProt 1–207 Author chain D； PDBConstruct 1–207； UniProt 1–207 Author chain E； PDBConstruct 1–207； UniProt 1–207 Author chain F； PDBConstruct 1–207； UniProt 1–207

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	2ekd
Deposition date deposition_date	2007-03-22
Structure title title	Structural study of Project ID PH0250 from Pyrococcus horikoshii OT3
Keywords keywords	;NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, STRUCTURAL GENOMICS, 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.

2ekd__assembly_1__model_1

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

Download this curve (.dat)

2ekd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ekd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.95 Å
Rg (electron density)	34.97 Å
Total Rg	35.68 Å
Atom count	9767
Residues	1195
Excluded volume	178370 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ekd__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ekd__assembly_2__model_1`	dodecameric （12）	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	Hypothetical protein PH0250
Molecular weight formula_weight	23848.0 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	10430

MQMNSEKFFKLFRVGETVLVEYSGTSRAELLLYYIVNNSKLPIVVDDILDTYYEFYTRLKVAGFDVAPLENVQVIKMGGTKDIGRVIGRLNISKYVISEQEYMEIVSQLKDYPVINPVLGLHKLILLGNTFENINVVKMVSNYVGREERIAFYFVNRNVIEKHSSPILDLLEEVVTSILEITDSGIIIKKSIKDEIAGKIVSPLLNF

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	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	663

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2ekdA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11570 — Protein of unknown function DUF257

Domain ID domain_id	2ekdB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11570 — Protein of unknown function DUF257

Domain ID domain_id	2ekdC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11570 — Protein of unknown function DUF257

Domain ID domain_id	2ekdD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11570 — Protein of unknown function DUF257

Domain ID domain_id	2ekdE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11570 — Protein of unknown function DUF257

Domain ID domain_id	2ekdF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11570 — Protein of unknown function DUF257

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Unit-cell length a length_a	93.471 Å
Unit-cell length b length_b	158.026 Å
Unit-cell length c length_c	163.347 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	48

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	29.940 Å
R factor r_factor	0.1900
R_work r_work	0.1880
R_free r_free	0.2250

Structural study of Project ID PH0250 from Pyrococcus horikoshii OT3

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

Hypothetical protein PH0250

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

2ekd__assembly_1__model_1

2ekd__assembly_1__model_1 | I(q)

2ekd__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)

Structural study of Project ID PH0250 from Pyrococcus horikoshii OT3

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

Hypothetical protein PH0250

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

2ekd__assembly_1__model_1

2ekd__assembly_1__model_1 | I(q)

2ekd__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)