SAXSdb — 1dku

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

PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 METHYL PHOSPHONIC ACID ADENOSINE ESTER × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 6 METHYL PHOSPHONIC ACID ADENOSINE ESTER × 6 water × 6	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 METHYL PHOSPHONIC ACID ADENOSINE ESTER × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KPRS_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–317； UniProt 1–317 Author chain B； PDBConstruct 1–317； UniProt 1–317

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	1dku
Deposition date deposition_date	1999-12-08
Structure title title	CRYSTAL STRUCTURES OF BACILLUS SUBTILIS PHOSPHORIBOSYLPYROPHOSPHATE SYNTHETASE: MOLECULAR BASIS OF ALLOSTERIC INHIBITION AND ACTIVATION.
Keywords keywords	OPEN ALPHA-BETA STRUCTURE, DOMAIN DUPLICATION, PHOSPHORIBOSYLTRANSFERASE TYPE I FOLD, 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.

1dku__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1dku__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1dku__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	28.69 Å
Rg (electron density)	27.98 Å
Total Rg	28.64 Å
Atom count	4644
Residues	590
Excluded volume	83281 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1dku__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1dku__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1dku__assembly_3__model_1`	dimeric （2）	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	PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
Molecular weight formula_weight	34910.2 kDa
EC 编号 ec_number	2.7.6.1
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	4824

MSNQYGDKNLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLEDIVIVSPDHGGVTRARKLADRLKAPIAIIDKRRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVHEQQSVSYLFS

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
Molecular weight formula_weight	425.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	METHYL PHOSPHONIC ACID ADENOSINE ESTER
Molecular weight formula_weight	345.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	180

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1dkua1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.2 — Phosphoribosylpyrophosphate synthetase-like

Domain ID domain_id	d1dkua2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.2 — Phosphoribosylpyrophosphate synthetase-like

Domain ID domain_id	d1dkub1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.2 — Phosphoribosylpyrophosphate synthetase-like

Domain ID domain_id	d1dkub2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.2 — Phosphoribosylpyrophosphate synthetase-like

CATH v4.4 (4 domains)

Domain ID domain_id	1dkuA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	1dkuA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	1dkuB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	1dkuB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

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Unit-cell length a length_a	115.650 Å
Unit-cell length b length_b	115.650 Å
Unit-cell length c length_c	106.410 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2410

CRYSTAL STRUCTURES OF BACILLUS SUBTILIS PHOSPHORIBOSYLPYROPHOSPHATE SYNTHETASE: MOLECULAR BASIS OF ALLOSTERIC INHIBITION AND ACTIVATION.

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

PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)

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

1dku__assembly_3__model_1

1dku__assembly_3__model_1 | I(q)

1dku__assembly_3__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)

CRYSTAL STRUCTURES OF BACILLUS SUBTILIS PHOSPHORIBOSYLPYROPHOSPHATE SYNTHETASE: MOLECULAR BASIS OF ALLOSTERIC INHIBITION AND ACTIVATION.

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

PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)

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

1dku__assembly_3__model_1

1dku__assembly_3__model_1 | I(q)

1dku__assembly_3__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)