SAXSdb — 2dc4

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

165aa long hypothetical protein

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	CHLORIDE ION × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O58740_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–165； UniProt 1–165 Author chain B； PDBConstruct 1–165； UniProt 1–165

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	2dc4
Deposition date deposition_date	2005-12-28
Structure title title	Structure of PH1012 protein from Pyrococcus Horikoshii OT3
Keywords keywords	;Dimer, Hypothetical Protein, 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.

2dc4__assembly_1__model_1

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

Download this curve (.dat)

2dc4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dc4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.08 Å
Rg (electron density)	25.46 Å
Total Rg	26.17 Å
Atom count	2767
Residues	328
Excluded volume	49907 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dc4__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 (3)

Entity 1 Entity 1 polymer

Description description	165aa long hypothetical protein
Molecular weight formula_weight	19609.5 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	3174

MEIEVKFRVNFEDIKRKIEGLGAKFFGIEEQEDVYFELPSPKLLRVRKINNTGKSYITYKEILDKRNEEFYELEFEVQDPEGAIELFKRLGFKVQGVVKKRRWIYKLNNVTFELNRVEKAGDFLDIEVITSNPEEGKKIIWDVARRLGLKEEDVEPKLYIELING

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	53953
Host organism host_organism	Escherichia coli BL21(DE3)

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	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	407

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2dc4a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.63 — CYTH-like phosphatases
Superfamily Superfamily superfamily	d.63.1 — CYTH-like phosphatases
Family Family family	d.63.1.2 — CYTH domain

Domain ID domain_id	d2dc4b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.63 — CYTH-like phosphatases
Superfamily Superfamily superfamily	d.63.1 — CYTH-like phosphatases
Family Family family	d.63.1.2 — CYTH domain

CATH v4.4 (2 domains)

Domain ID domain_id	2dc4A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	320 — Hypothetical Protein Pfu-838710-001
Homologous superfamily homologous superfamily	10 — Hypothetical Protein Pfu-838710-001

Domain ID domain_id	2dc4B00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	320 — Hypothetical Protein Pfu-838710-001
Homologous superfamily homologous superfamily	10 — Hypothetical Protein Pfu-838710-001

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Unit-cell length a length_a	53.123 Å
Unit-cell length b length_b	53.123 Å
Unit-cell length c length_c	111.147 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	6

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	26.560 Å
R factor r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2360

Structure of PH1012 protein from Pyrococcus Horikoshii OT3

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

165aa long hypothetical protein

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

2dc4__assembly_1__model_1

2dc4__assembly_1__model_1 | I(q)

2dc4__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of PH1012 protein from Pyrococcus Horikoshii OT3

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

165aa long hypothetical protein

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

2dc4__assembly_1__model_1

2dc4__assembly_1__model_1 | I(q)

2dc4__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)