SAXSdb — 2dek

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

Probable diphthine synthase

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SODIUM ION × 1 S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	SODIUM ION × 2 S-ADENOSYL-L-HOMOCYSTEINE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPHB_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–265； UniProt 1–265 Author chain B； PDBConstruct 1–265； UniProt 1–265

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	2dek
Deposition date deposition_date	2006-02-10
Structure title title	Crystal structure of project ID PH0725 from Pyrococcus horikoshii OT3 at 1.65 A resolution
Keywords keywords	;ALPHA/BETA FOLD, ANTIPARALLEL BETA-SHEET, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Transferase ;; TRANSFERASE
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.

2dek__assembly_1__model_1

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

Download this curve (.dat)

2dek__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dek__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.09 Å
Rg (electron density)	22.71 Å
Total Rg	23.75 Å
Atom count	4199
Residues	530
Excluded volume	75969 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dek__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2dek__assembly_2__model_1`	tetrameric （4）	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	Probable diphthine synthase
Molecular weight formula_weight	29613.4 kDa
EC 编号 ec_number	2.1.1.98
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4858

MVLYFIGLGLYDERDITVKGLEIAKKCDYVFAEFYTSLMAGTTLGRIQKLIGKEIRVLSREDVELNFENIVLPLAKENDVAFLTPGDPLVATTHAELRIRAKRAGVESYVIHAPSIYSAVGITGLHIYKFGKSATVAYPEGNWFPTSYYDVIKENAERGLHTLLFLDIKAEKRMYMTANEAMELLLKVEDMKKGGVFTDDTLVVVLARAGSLNPTIRAGYVKDLIREDFGDPPHILIVPGKLHIVEAEYLVEIAGAPREILRVNV

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	1

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	606

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2deka_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.90 — Tetrapyrrole methylase
Superfamily Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
Family Family family	c.90.1.0 — automated matches

Domain ID domain_id	d2dekb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.90 — Tetrapyrrole methylase
Superfamily Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
Family Family family	c.90.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2dekA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
Homologous superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

Domain ID domain_id	2dekA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
Homologous superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

Domain ID domain_id	2dekB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
Homologous superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

Domain ID domain_id	2dekB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
Homologous superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

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Unit-cell length a length_a	104.500 Å
Unit-cell length b length_b	104.500 Å
Unit-cell length c length_c	137.660 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	16

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	29.790 Å
R factor r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2240

Crystal structure of project ID PH0725 from Pyrococcus horikoshii OT3 at 1.65 A resolution

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

Probable diphthine synthase

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

2dek__assembly_1__model_1

2dek__assembly_1__model_1 | I(q)

2dek__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of project ID PH0725 from Pyrococcus horikoshii OT3 at 1.65 A resolution

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

Probable diphthine synthase

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

2dek__assembly_1__model_1

2dek__assembly_1__model_1 | I(q)

2dek__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)