SAXSdb — 6hf6

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

Deglycase PH1704

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

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 MALONATE ION × 6 TERBIUM(III) ION × 8 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	6hf6
Deposition date deposition_date	2018-08-21
Structure title title	Crystal structure of the Protease 1 (E29A,E60A,E80A) from Pyrococcus horikoshii co-crystallized with Tb-Xo4.
Keywords keywords	;meshandcollect, de novo phasing, SAD, crystallization, Tb-Xo4, crystallophore, Lanthanide complex, multi-crystals data collection, ccCluster, HYDROLASE ;; HYDROLASE
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.

6hf6__assembly_1__model_1

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

Download this curve (.dat)

6hf6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6hf6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.98 Å
Rg (electron density)	31.25 Å
Total Rg	31.84 Å
Atom count	15992
Residues	996
Excluded volume	144460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6hf6__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 (5)

Entity 1 Entity 1 polymer

Description description	Deglycase PH1704
Molecular weight formula_weight	18476.3 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	8605

MKVLFLTANEFEDVELIYPYHRLKEEGHAVYIASFERGTITGKHGYSVKVDLTFDKVNPAEFDALVLPGGRAPERVRLNAKAVSIARKMFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDMINAGVEWVDAEVVVDGNWVSSRVPADLYAWMREFVKLLK

Source Source

Source organism organism	Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli

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	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	3

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	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	552

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d6hf6a_
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	d6hf6b_
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	d6hf6c_
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	6hf6A00
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	6hf6B00
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	6hf6C00
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	124.620 Å
Unit-cell length b length_b	124.620 Å
Unit-cell length c length_c	130.310 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	2.000 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.1630
R_work r_work	0.1620
R_free r_free	0.1810

Crystal structure of the Protease 1 (E29A,E60A,E80A) from Pyrococcus horikoshii co-crystallized with Tb-Xo4.

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

6hf6__assembly_1__model_1

6hf6__assembly_1__model_1 | I(q)

6hf6__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of the Protease 1 (E29A,E60A,E80A) from Pyrococcus horikoshii co-crystallized with Tb-Xo4.

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

6hf6__assembly_1__model_1

6hf6__assembly_1__model_1 | I(q)

6hf6__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)