SAXSdb — 1k23

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

Manganese-dependent inorganic pyrophosphatase

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	MANGANESE (II) ION × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPAC_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–309； UniProt 1–309 Author chain B； PDBConstruct 1–309； UniProt 1–309 Author chain C； PDBConstruct 1–309； UniProt 1–309 Author chain D； PDBConstruct 1–309； UniProt 1–309

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	1k23
Deposition date deposition_date	2001-09-26
Structure title title	Inorganic Pyrophosphatase (Family II) from Bacillus subtilis
Keywords keywords	inorganic pyrophosphatase, manganese, binuclear metal centre, HYDROLASE; HYDROLASE
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.

1k23__assembly_1__model_1

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

Download this curve (.dat)

1k23__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1k23__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.60 Å
Rg (electron density)	33.30 Å
Total Rg	33.47 Å
Atom count	4746
Residues	604
Excluded volume	85399 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1k23__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1k23__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Manganese-dependent inorganic pyrophosphatase
Molecular weight formula_weight	34260.2 kDa
EC 编号 ec_number	3.6.1.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8973

MEKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAMAE

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	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	58

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1k23a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.107 — DHH phosphoesterases
Superfamily Superfamily superfamily	c.107.1 — DHH phosphoesterases
Family Family family	c.107.1.1 — Manganese-dependent inorganic pyrophosphatase (family II)

Domain ID domain_id	d1k23b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.107 — DHH phosphoesterases
Superfamily Superfamily superfamily	c.107.1 — DHH phosphoesterases
Family Family family	c.107.1.1 — Manganese-dependent inorganic pyrophosphatase (family II)

Domain ID domain_id	d1k23c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.107 — DHH phosphoesterases
Superfamily Superfamily superfamily	c.107.1 — DHH phosphoesterases
Family Family family	c.107.1.1 — Manganese-dependent inorganic pyrophosphatase (family II)

Domain ID domain_id	d1k23d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.107 — DHH phosphoesterases
Superfamily Superfamily superfamily	c.107.1 — DHH phosphoesterases
Family Family family	c.107.1.1 — Manganese-dependent inorganic pyrophosphatase (family II)

CATH v4.4 (7 domains)

Domain ID domain_id	1k23A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1640 — inorganic pyrophosphatase (n-terminal core)
Homologous superfamily homologous superfamily	10 — inorganic pyrophosphatase (n-terminal core)

Domain ID domain_id	1k23A02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — DHHA2 domain

Domain ID domain_id	1k23B01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1640 — inorganic pyrophosphatase (n-terminal core)
Homologous superfamily homologous superfamily	10 — inorganic pyrophosphatase (n-terminal core)

Domain ID domain_id	1k23B02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — DHHA2 domain

Domain ID domain_id	1k23C01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1640 — inorganic pyrophosphatase (n-terminal core)
Homologous superfamily homologous superfamily	10 — inorganic pyrophosphatase (n-terminal core)

Domain ID domain_id	1k23C02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — DHHA2 domain

Domain ID domain_id	1k23D01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1640 — inorganic pyrophosphatase (n-terminal core)
Homologous superfamily homologous superfamily	10 — inorganic pyrophosphatase (n-terminal core)

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Unit-cell length a length_a	80.290 Å
Unit-cell length b length_b	130.560 Å
Unit-cell length c length_c	150.470 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	19.960 Å
R factor r_factor	—
R_work r_work	0.2600
R_free r_free	0.2930

Inorganic Pyrophosphatase (Family II) from Bacillus subtilis

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

Manganese-dependent inorganic pyrophosphatase

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

1k23__assembly_1__model_1

1k23__assembly_1__model_1 | I(q)

1k23__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 11 domains

SCOP 2.08 (4 domains)

CATH v4.4 (7 domains)

7. Citations (1)

Inorganic Pyrophosphatase (Family II) from Bacillus subtilis

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

Manganese-dependent inorganic pyrophosphatase

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

1k23__assembly_1__model_1

1k23__assembly_1__model_1 | I(q)

1k23__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 11 domains

SCOP 2.08 (4 domains)

CATH v4.4 (7 domains)

7. Citations (1)