SAXSdb — 2d16

▼

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

hypothetical protein PH1918

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SODIUM ION × 4 GLYCEROL × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	SODIUM ION × 6 GLYCEROL × 6 water × 6	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 6	SODIUM ION × 6 GLYCEROL × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O59581_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–162； UniProt 1–162 Author chain B； PDBConstruct 1–162； UniProt 1–162 Author chain C； PDBConstruct 1–162； UniProt 1–162 Author chain D； PDBConstruct 1–162； UniProt 1–162

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2d16
Deposition date deposition_date	2005-08-14
Structure title title	Crystal Structure of PH1918 protein from Pyrococcus horikoshii OT3
Keywords keywords	;Hypothetical, 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

▼

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.

2d16__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2d16__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2d16__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	28.11 Å
Rg (electron density)	26.75 Å
Total Rg	27.81 Å
Atom count	7460
Residues	969
Excluded volume	134800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2d16__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2d16__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2d16__assembly_3__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	hypothetical protein PH1918
Molecular weight formula_weight	17662.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5572

MVRIEVIDIEKPEGVEVIIGQGNFSIFTVDDLARALLTAVPGIKFGIAMNEAKPQLTRYTGNDPELEALAAKNAVKIGAGHVFVILMKNAYPINVLNTIKNHPAVAMIYGASENPFQVIVAETELGRAVIGVVDGKAANKIETDEQKKERRELVEKIGYKID

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	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	596

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2d16a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.256 — Ta1353-like
Superfamily Superfamily superfamily	d.256.1 — Ta1353-like
Family Family family	d.256.1.0 — automated matches

Domain ID domain_id	d2d16b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.256 — Ta1353-like
Superfamily Superfamily superfamily	d.256.1 — Ta1353-like
Family Family family	d.256.1.0 — automated matches

Domain ID domain_id	d2d16c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.256 — Ta1353-like
Superfamily Superfamily superfamily	d.256.1 — Ta1353-like
Family Family family	d.256.1.0 — automated matches

Domain ID domain_id	d2d16d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.256 — Ta1353-like
Superfamily Superfamily superfamily	d.256.1 — Ta1353-like
Family Family family	d.256.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2d16A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1520 — hypothetical protein tt1634
Homologous superfamily homologous superfamily	10 — Ta1353-like

Domain ID domain_id	2d16B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1520 — hypothetical protein tt1634
Homologous superfamily homologous superfamily	10 — Ta1353-like

Domain ID domain_id	2d16C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1520 — hypothetical protein tt1634
Homologous superfamily homologous superfamily	10 — Ta1353-like

Domain ID domain_id	2d16D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1520 — hypothetical protein tt1634
Homologous superfamily homologous superfamily	10 — Ta1353-like

▶

Unit-cell length a length_a	66.120 Å
Unit-cell length b length_b	66.120 Å
Unit-cell length c length_c	125.072 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	12

Space group space_group	P 3
Space-group number int_tables_number	143
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	33.700 Å
R factor r_factor	0.1850
R_work r_work	0.1850
R_free r_free	0.2040

Crystal Structure of PH1918 protein from Pyrococcus horikoshii OT3

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

hypothetical protein PH1918

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

2d16__assembly_2__model_1

2d16__assembly_2__model_1 | I(q)

2d16__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of PH1918 protein from Pyrococcus horikoshii OT3

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

hypothetical protein PH1918

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

2d16__assembly_2__model_1

2d16__assembly_2__model_1 | I(q)

2d16__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)