SAXSdb — 1k20

▼

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

Manganese-dependent inorganic pyrophosphatase

Streptococcus gordonii

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 SULFATE ION × 4 GLYCEROL × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPAC_STRGC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–310； UniProt 2–311 Author chain B； PDBConstruct 1–310； UniProt 2–311

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1k20
Deposition date deposition_date	2001-09-26
Structure title title	Inorganic Pyrophosphatase (family II) from Streptococcus gordonii at 1.5 A resolution
Keywords keywords	Family II PPase, Manganese, Binuclear Metal Centre, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1k20__assembly_1__model_1

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

Download this curve (.dat)

1k20__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1k20__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.45 Å
Rg (electron density)	25.77 Å
Total Rg	26.49 Å
Atom count	4748
Residues	620
Excluded volume	84305 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1k20__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Manganese-dependent inorganic pyrophosphatase
Molecular weight formula_weight	33437.4 kDa
EC 编号 ec_number	3.6.1.1
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	5424

SKILVFGHQNPDSDAIGSSYAFAYLAREAYGLDTEAVALGEPNEETAFVLDYFGVAAPRVITSAKAEGAEQVILTDHNEFQQSVADIAEVEVYGVVDHHRVANFETANPLYMRLEPVGSASSIVYRMFKEHSVAVSKEIAGLMLSGLISDTLLLKSPTTHPTDKAIAPELAELAGVNLEEYGLAMLKAGTNLASKSAEELIDIDAKTFELNGNNVRVAQVNTVDIAEVLERQAEIEAAIEKAIADNGYSDFVLMITDIINSNSEILAIGSNMDKVEAAFNFVLENNHAFLAGAVSRKKQVVPQLTESFNA

Source Source

Source organism organism	Streptococcus gordonii
NCBI taxonomy ID ncbi_taxonomy_id	1302
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	4

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	676

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1k20a_
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	d1k20b_
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 (4 domains)

Domain ID domain_id	1k20A01
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	1k20A02
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	1k20B01
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	1k20B02
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

▶

Unit-cell length a length_a	60.197 Å
Unit-cell length b length_b	87.552 Å
Unit-cell length c length_c	130.027 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	1.500 Å
Low-resolution limit resolution_low	29.320 Å
R factor r_factor	—
R_work r_work	0.1750
R_free r_free	0.1880

Inorganic Pyrophosphatase (family II) from Streptococcus gordonii at 1.5 A resolution

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

1k20__assembly_1__model_1

1k20__assembly_1__model_1 | I(q)

1k20__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Inorganic Pyrophosphatase (family II) from Streptococcus gordonii at 1.5 A resolution

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

1k20__assembly_1__model_1

1k20__assembly_1__model_1 | I(q)

1k20__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)