2gfq

Structure of Protein of Unknown Function PH0006 from Pyrococcus horikoshii

Method: X-RAY DIFFRACTION

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

UPF0204 protein PH0006

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	SULFATE ION × 17 MAGNESIUM ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y006_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–296； UniProt 1–274 Author chain B； PDBConstruct 23–296； UniProt 1–274 Author chain C； PDBConstruct 23–296； UniProt 1–274

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	2gfq
Deposition date deposition_date	2006-03-22
Structure title title	Structure of Protein of Unknown Function PH0006 from Pyrococcus horikoshii
Keywords keywords	;Pyrococcus horikoshii, ph0006, Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, 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.

2gfq__assembly_1__model_1

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

Download this curve (.dat)

2gfq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2gfq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.43 Å
Rg (electron density)	35.08 Å
Total Rg	35.46 Å
Atom count	6807
Residues	819
Excluded volume	121520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2gfq__assembly_1__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	UPF0204 protein PH0006
Molecular weight formula_weight	34080.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7927

MGSSHHHHHHSSGRENLYFQGHMKVIMTTKVDKASMNIMNKLIENFGFKETEYVFEGNPVYKRGDVLILTTNDEMIYYDYLDREIENQLGFKPEIIAFASRHSSKQKLPALTTHVTGNWGKAMYGGKDESFAVAIPSAMKLSLLKMSELNDLGWTVCYEATHHGPTELEVPSFFIEIGSSEEEWINDRAGEIIAETIIYVLDNYEKGRSKFKVALGIGGGHYAPKQTKRALEGDLAFGHILPKYAQPVSRDVMIKALNRFGEKVEAIYVDWKGSRGETRQLAKSLAQELGLEFIKDGS

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli BL21(DE3)

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	17

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1036

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d2gfqa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.7 — AF0625-like
Family Family family	c.56.7.1 — AF0625-like

Domain ID domain_id	d2gfqa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2gfqa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2gfqb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.7 — AF0625-like
Family Family family	c.56.7.1 — AF0625-like

Domain ID domain_id	d2gfqb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2gfqb4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2gfqc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.7 — AF0625-like
Family Family family	c.56.7.1 — AF0625-like

Domain ID domain_id	d2gfqc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2gfqc4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	2gfqA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	50 — AF0625-like

Domain ID domain_id	2gfqA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10700 — AF0625-like

Domain ID domain_id	2gfqB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	50 — AF0625-like

Domain ID domain_id	2gfqB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10700 — AF0625-like

Domain ID domain_id	2gfqC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	50 — AF0625-like

Domain ID domain_id	2gfqC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10700 — AF0625-like

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Unit-cell length a length_a	65.021 Å
Unit-cell length b length_b	67.029 Å
Unit-cell length c length_c	111.572 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.09 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	35.800 Å
R factor r_factor	0.1519
R_work r_work	0.1505
R_free r_free	0.1790

Structure of Protein of Unknown Function PH0006 from Pyrococcus horikoshii

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

UPF0204 protein PH0006

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

2gfq__assembly_1__model_1

2gfq__assembly_1__model_1 | I(q)

2gfq__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 (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) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structure of Protein of Unknown Function PH0006 from Pyrococcus horikoshii

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

UPF0204 protein PH0006

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

2gfq__assembly_1__model_1

2gfq__assembly_1__model_1 | I(q)

2gfq__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 (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) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)