SAXSdb — 8acu

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

GTP pyrophosphokinase

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	CBS domain-containing protein × 2 （A0A164SLA6） MANGANESE (II) ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RELA_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–373； UniProt 1–373 Author chain B； PDBConstruct 1–373； UniProt 1–373

CBS domain-containing protein

Bacillus subtilis

UniProt A0A164SLA6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	GTP pyrophosphokinase × 2 （O54408） MANGANESE (II) ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A164SLA6_BACIU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–147； UniProt 1–147 Author chain F； PDBConstruct 1–147； UniProt 1–147

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	8acu
Deposition date deposition_date	2022-07-06
Structure title title	Structure of Bacillus subtilis Rel in complex with DarB
Keywords keywords	Rel, GTP pyrophosphokinase, DarB, CBPB, stringent factor, translation, ribosome, 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.

8acu__assembly_1__model_1

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

Download this curve (.dat)

8acu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8acu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.43 Å
Rg (electron density)	40.41 Å
Total Rg	40.19 Å
Atom count	7171
Residues	959
Excluded volume	127360 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8acu__assembly_1__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	GTP pyrophosphokinase
Molecular weight formula_weight	43479.0 kDa
EC 编号 ec_number	2.7.6.5
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	7219

MANEQVLTAEQVIDKARSYLSDEHIAFVEKAYLYAEDAHREQYRKSGEPYIIHPIQVAGILVDLEMDPSTIAGGFLHDVVEDTDVTLDDLKEAFSEEVAMLVDGVTKLGKIKYKSQEEQQAENHRKMFVAMAQDIRVILIKLADRLHNMRTLKHLPQEKQRRISNETLEIFAPLAHRLGISKIKWELEDTALRYLNPQQYYRIVNLMKKKRAERELYVDEVVNEVKKRVEEVNIKADFSGRPKHIYSIYRKMVLQNKQFNEIYDLLAVRILVNSIKDCYAVLGIIHTCWKPMPGRFKDYIAMPKPNMYQSLHTTVIGPKGDPLEVQIRTFEMHEIAEYGVAAHWAYKEGKAANEGATFEKKLSWFREILEFQN

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	CBS domain-containing protein
Molecular weight formula_weight	16653.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

MISLQSDQLLEATVGQFMIEADKVAHVQVGNNLEHALLVLTKTGYTAIPVLDPSYRLHGLIGTNMIMNSIFGLERIEFEKLDQITVEEVMLTDIPRLHINDPIMKGFGMVINNGFVCVENDEQVFEGIFTRRVVLKELNKHIRSLNK

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 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	42

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	8acuA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	8acuA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	8acuB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	8acuB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

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Unit-cell length a length_a	94.401 Å
Unit-cell length b length_b	98.141 Å
Unit-cell length c length_c	126.775 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.970 Å
Low-resolution limit resolution_low	75.720 Å
R factor r_factor	0.2627
R_work r_work	0.2601
R_free r_free	0.3153

Structure of Bacillus subtilis Rel in complex with DarB

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

GTP pyrophosphokinase

State in the Current Structure

Other States of the Same Protein in the Database

CBS domain-containing protein

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

8acu__assembly_1__model_1

8acu__assembly_1__model_1 | I(q)

8acu__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of Bacillus subtilis Rel in complex with DarB

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

GTP pyrophosphokinase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CBS domain-containing protein

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

8acu__assembly_1__model_1

8acu__assembly_1__model_1 | I(q)

8acu__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)