2dtt

Crystal structure of 6-pyruvoyl tetrahydrobiopterin synthase from Pyrococcus horikoshii OT3 complexed with (1'R,2'S)-biopterin

Method: X-RAY DIFFRACTION

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

Hypothetical protein PH0634

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	5,6,7,8-TETRAHYDROBIOPTERIN × 3 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	5,6,7,8-TETRAHYDROBIOPTERIN × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O58368_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–115； UniProt 1–115 Author chain B； PDBConstruct 1–115； UniProt 1–115 Author chain C； PDBConstruct 1–115； UniProt 1–115 Author chain D； PDBConstruct 1–115； UniProt 1–115 Author chain E； PDBConstruct 1–115； UniProt 1–115 Author chain F； PDBConstruct 1–115； UniProt 1–115

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	2dtt
Deposition date deposition_date	2006-07-15
Structure title title	Crystal structure of 6-pyruvoyl tetrahydrobiopterin synthase from Pyrococcus horikoshii OT3 complexed with (1'R,2'S)-biopterin
Keywords keywords	;6-pyruvoyl tetrahydrobiopterin synthase (PTPS), Biopterin, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, LYASE ;; LYASE
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.

2dtt__assembly_2__model_1

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

Download this curve (.dat)

2dtt__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dtt__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.03 Å
Rg (electron density)	20.73 Å
Total Rg	21.57 Å
Atom count	2750
Residues	324
Excluded volume	49037 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dtt__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2dtt__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Hypothetical protein PH0634
Molecular weight formula_weight	13532.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	5910

MKSRIIVRTSFDAAHAVKVGDHWEDVHGHTFFLEVAIEGEIKNGYVMDFLELRKIVEEITKELDHRNLNNIFENPTTENIALWIGERIRDKLPPYVKLKRVVLWEGKDNGVELEW

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	5,6,7,8-TETRAHYDROBIOPTERIN
Molecular weight formula_weight	241.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	405

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2dtta_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.0 — automated matches

Domain ID domain_id	d2dttb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.0 — automated matches

Domain ID domain_id	d2dttc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.0 — automated matches

Domain ID domain_id	d2dttd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.0 — automated matches

Domain ID domain_id	d2dtte_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.0 — automated matches

Domain ID domain_id	d2dttf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	2dttA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	479 — Tetrahydropterin Synthase; Chain A
Homologous superfamily homologous superfamily	10 — 6-pyruvoyl tetrahydropterin synthase/QueD

Domain ID domain_id	2dttB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	479 — Tetrahydropterin Synthase; Chain A
Homologous superfamily homologous superfamily	10 — 6-pyruvoyl tetrahydropterin synthase/QueD

Domain ID domain_id	2dttC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	479 — Tetrahydropterin Synthase; Chain A
Homologous superfamily homologous superfamily	10 — 6-pyruvoyl tetrahydropterin synthase/QueD

Domain ID domain_id	2dttD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	479 — Tetrahydropterin Synthase; Chain A
Homologous superfamily homologous superfamily	10 — 6-pyruvoyl tetrahydropterin synthase/QueD

Domain ID domain_id	2dttE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	479 — Tetrahydropterin Synthase; Chain A
Homologous superfamily homologous superfamily	10 — 6-pyruvoyl tetrahydropterin synthase/QueD

Domain ID domain_id	2dttF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	479 — Tetrahydropterin Synthase; Chain A
Homologous superfamily homologous superfamily	10 — 6-pyruvoyl tetrahydropterin synthase/QueD

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Unit-cell length a length_a	35.682 Å
Unit-cell length b length_b	105.445 Å
Unit-cell length c length_c	96.147 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.95 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	35.680 Å
R factor r_factor	0.1950
R_work r_work	0.1950
R_free r_free	0.2360

Crystal structure of 6-pyruvoyl tetrahydrobiopterin synthase from Pyrococcus horikoshii OT3 complexed with (1'R,2'S)-biopterin

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

Hypothetical protein PH0634

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

2dtt__assembly_2__model_1

2dtt__assembly_2__model_1 | I(q)

2dtt__assembly_2__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of 6-pyruvoyl tetrahydrobiopterin synthase from Pyrococcus horikoshii OT3 complexed with (1'R,2'S)-biopterin

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

Hypothetical protein PH0634

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

2dtt__assembly_2__model_1

2dtt__assembly_2__model_1 | I(q)

2dtt__assembly_2__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)