2zau

Crystal structure of an N-terminally truncated selenophosphate synthetase from Aquifex aeolicus

Method: X-RAY DIFFRACTION

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

Selenide, water dikinase

Aquifex aeolicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	PHOSPHATE ION × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SELD_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–311； UniProt 27–336 Author chain B； PDBConstruct 2–311； UniProt 27–336 Author chain C； PDBConstruct 2–311； UniProt 27–336

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	2zau
Deposition date deposition_date	2007-10-10
Structure title title	Crystal structure of an N-terminally truncated selenophosphate synthetase from Aquifex aeolicus
Keywords keywords	;INTRAMOLECULAR S-S BOND, TRIMER OF DIMERS, ATP-binding, Kinase, Magnesium, Nucleotide-binding, Selenium, Selenocysteine, Transferase, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; 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.

2zau__assembly_1__model_1

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

Download this curve (.dat)

2zau__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zau__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.51 Å
Rg (electron density)	41.33 Å
Total Rg	41.79 Å
Atom count	14184
Residues	1828
Excluded volume	256100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zau__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 (3)

Entity 1 Entity 1 polymer

Description description	Selenide, water dikinase
Molecular weight formula_weight	34263.4 kDa
EC 编号 ec_number	2.7.9.3
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	7533

MKGFNIYTDESTLVSIGDDAGVYEHNGIIWVYTVDIITPVVNDPYLWGAISTANALSDVYAMGGIPVNALAISCFNNCELDIEIFREVIRGALDKLREAKTVLLGGHTIDDKEPKFGLSVAGICPEGKYITQSGAQVGQLLILTKPIGTGILIKGLKEGILKEEDINEAIENMLALNDKARNLMLSLDATACTDVTGFGLLGHAWNICKNSNIGARIFFEKVPYYQLSENLVKKKIYPKGAIENLNFVKNYLKSNLDNWKLILLSDPVTSGGLLFTINKEKLEKIDETAKELEVNYWIIGETIAENVLEVL

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	441

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2zaua1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.4 — PurM N-terminal domain-like
Family Family family	d.79.4.1 — PurM N-terminal domain-like

Domain ID domain_id	d2zaua2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.139 — PurM C-terminal domain-like
Superfamily Superfamily superfamily	d.139.1 — PurM C-terminal domain-like
Family Family family	d.139.1.1 — PurM C-terminal domain-like

Domain ID domain_id	d2zaub1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.4 — PurM N-terminal domain-like
Family Family family	d.79.4.1 — PurM N-terminal domain-like

Domain ID domain_id	d2zaub2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.139 — PurM C-terminal domain-like
Superfamily Superfamily superfamily	d.139.1 — PurM C-terminal domain-like
Family Family family	d.139.1.1 — PurM C-terminal domain-like

Domain ID domain_id	d2zauc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.4 — PurM N-terminal domain-like
Family Family family	d.79.4.1 — PurM N-terminal domain-like

Domain ID domain_id	d2zauc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.139 — PurM C-terminal domain-like
Superfamily Superfamily superfamily	d.139.1 — PurM C-terminal domain-like
Family Family family	d.139.1.1 — PurM C-terminal domain-like

CATH v4.4 (6 domains)

Domain ID domain_id	2zauA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	10 — PurM-like, N-terminal domain

Domain ID domain_id	2zauA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	650 — Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — PurM-like C-terminal domain

Domain ID domain_id	2zauB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	10 — PurM-like, N-terminal domain

Domain ID domain_id	2zauB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	650 — Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — PurM-like C-terminal domain

Domain ID domain_id	2zauC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	10 — PurM-like, N-terminal domain

Domain ID domain_id	2zauC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	650 — Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — PurM-like C-terminal domain

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Unit-cell length a length_a	93.161 Å
Unit-cell length b length_b	165.198 Å
Unit-cell length c length_c	167.684 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	46.290 Å
R factor r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2390

Crystal structure of an N-terminally truncated selenophosphate synthetase from Aquifex aeolicus

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

Selenide, water dikinase

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

2zau__assembly_1__model_1

2zau__assembly_1__model_1 | I(q)

2zau__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 (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 an N-terminally truncated selenophosphate synthetase from Aquifex aeolicus

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

Selenide, water dikinase

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

2zau__assembly_1__model_1

2zau__assembly_1__model_1 | I(q)

2zau__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 (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)