SAXSdb — 1wcf

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

INORGANIC PYROPHOSPHATASE

MYCOBACTERIUM TUBERCULOSIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	POTASSIUM ION × 12 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	IPYR_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–171； UniProt 1–162

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	1wcf
Deposition date deposition_date	2004-11-13
Structure title title	1.54 A CRYSTAL STRUCTURE OF RV3628, MYCOBACTERIUM TUBERCULOSIS INORGANIC PYROPHOSPHATASE (PPASE) AT PH7.0
Keywords keywords	STRUCTURAL GENOMICS, POTASSIUM, 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.

1wcf__assembly_1__model_1

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

Download this curve (.dat)

1wcf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wcf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.91 Å
Rg (electron density)	28.34 Å
Total Rg	29.27 Å
Atom count	7722
Residues	972
Excluded volume	137080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wcf__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 (4)

Entity 1 Entity 1 polymer

Description description	INORGANIC PYROPHOSPHATASE
Molecular weight formula_weight	19486.9 kDa
EC 编号 ec_number	3.6.1.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1596

MSSHHHHHHMQFDVTIEIPKGQRNKYEVDHETGRVRLDRYLYTPMAYPTDYGFIEDTLGDDGDPLDALVLLPQPVFPGVLVAARPVGMFRMVDEHGGDDKVLCVPAGDPRWDHVQDIGDVPAFELDAIKHFFVHYKDLEPGKFVKAADWVDRAEAEAEVQRSVERFKAGTH

Source Source

Source organism organism	MYCOBACTERIUM TUBERCULOSIS
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	279

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1wcfa1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.5 — Inorganic pyrophosphatase
Family Family family	b.40.5.0 — automated matches

Domain ID domain_id	d1wcfa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1wcfA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

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Unit-cell length a length_a	96.902 Å
Unit-cell length b length_b	96.902 Å
Unit-cell length c length_c	103.312 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 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	1.540 Å
Low-resolution limit resolution_low	84.520 Å
R factor r_factor	0.1570
R_work r_work	0.1560
R_free r_free	0.1700

1.54 A CRYSTAL STRUCTURE OF RV3628, MYCOBACTERIUM TUBERCULOSIS INORGANIC PYROPHOSPHATASE (PPASE) AT PH7.0

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

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

1wcf__assembly_1__model_1

1wcf__assembly_1__model_1 | I(q)

1wcf__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

1.54 A CRYSTAL STRUCTURE OF RV3628, MYCOBACTERIUM TUBERCULOSIS INORGANIC PYROPHOSPHATASE (PPASE) AT PH7.0

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

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

1wcf__assembly_1__model_1

1wcf__assembly_1__model_1 | I(q)

1wcf__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)