SAXSdb — 6f2f

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

Deglycase PH1704

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	Tb-Xo4 × 6 SULFATE ION × 16 TERBIUM(III) ION × 2 Dihydroxyacetone × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DEGLY_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–166； UniProt 1–166 Author chain B； PDBConstruct 1–166； UniProt 1–166 Author chain C； PDBConstruct 1–166； UniProt 1–166

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	6f2f
Deposition date deposition_date	2017-11-24
Structure title title	Crystal structure of Protease 1 from Pyrococcus Horikoshii co-cystallized in presence of 10 mM Tb-Xo4 and ammonium sulfate.
Keywords keywords	Lanthanide complexes, Tb-Xo4, Crystallophore, Phasing, nucleation, CELL CYCLE; CELL CYCLE
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.

6f2f__assembly_1__model_1

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

Download this curve (.dat)

6f2f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6f2f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.34 Å
Rg (electron density)	31.41 Å
Total Rg	32.17 Å
Atom count	16184
Residues	996
Excluded volume	145690 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6f2f__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 (6)

Entity 1 Entity 1 polymer

Description description	Deglycase PH1704
Molecular weight formula_weight	18650.4 kDa
EC 编号 ec_number	3.5.1.124,3.4.22.-
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	8784

MKVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFERGTITGKHGYSVKVDLTFDKVNPEEFDALVLPGGRAPERVRLNEKAVSIARKMFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDMINAGVEWVDAEVVVDGNWVSSRVPADLYAWMREFVKLLK

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	Tb-Xo4
Molecular weight formula_weight	556.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	TERBIUM(III) ION
Molecular weight formula_weight	158.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	Dihydroxyacetone
Molecular weight formula_weight	90.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	614

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d6f2fa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
Family Family family	c.23.16.2 — DJ-1/PfpI

Domain ID domain_id	d6f2fb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
Family Family family	c.23.16.2 — DJ-1/PfpI

Domain ID domain_id	d6f2fc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
Family Family family	c.23.16.2 — DJ-1/PfpI

CATH v4.4 (3 domains)

Domain ID domain_id	6f2fA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

Domain ID domain_id	6f2fB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

Domain ID domain_id	6f2fC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

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Unit-cell length a length_a	124.588 Å
Unit-cell length b length_b	124.588 Å
Unit-cell length c length_c	128.866 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	24

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	44.770 Å
R factor r_factor	0.1610
R_work r_work	0.1610
R_free r_free	0.1700

Crystal structure of Protease 1 from Pyrococcus Horikoshii co-cystallized in presence of 10 mM Tb-Xo4 and ammonium sulfate.

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

Deglycase PH1704

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

6f2f__assembly_1__model_1

6f2f__assembly_1__model_1 | I(q)

6f2f__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of Protease 1 from Pyrococcus Horikoshii co-cystallized in presence of 10 mM Tb-Xo4 and ammonium sulfate.

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

Deglycase PH1704

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

6f2f__assembly_1__model_1

6f2f__assembly_1__model_1 | I(q)

6f2f__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)