SAXSdb — 3emj

▼

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

Inorganic pyrophosphatase

Rickettsia prowazekii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	TETRAETHYLENE GLYCOL × 1 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	TETRAETHYLENE GLYCOL × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IPYR_RICPR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–173； UniProt 1–172 Author chain B； PDBConstruct 2–173； UniProt 1–172 Author chain C； PDBConstruct 2–173； UniProt 1–172 Author chain D； PDBConstruct 2–173； UniProt 1–172 Author chain E； PDBConstruct 2–173； UniProt 1–172 Author chain F； PDBConstruct 2–173； UniProt 1–172 Author chain G； PDBConstruct 2–173； UniProt 1–172 Author chain H； PDBConstruct 2–173； UniProt 1–172 Author chain I； PDBConstruct 2–173； UniProt 1–172 Author chain J； PDBConstruct 2–173； UniProt 1–172 Author chain K； PDBConstruct 2–173； UniProt 1–172 Author chain L； PDBConstruct 2–173； UniProt 1–172

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	3emj
Deposition date deposition_date	2008-09-24
Structure title title	2.2 A crystal structure of inorganic pyrophosphatase from rickettsia prowazekii (p21 form)
Keywords keywords	;RICKETTSIA, INORGANIC PYROPHOSPHATASE, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, SSGCID, Cytoplasm, Hydrolase, Magnesium, Metal-binding ;; 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.

3emj__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3emj__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3emj__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.97 Å
Rg (electron density)	28.50 Å
Total Rg	29.45 Å
Atom count	7861
Residues	989
Excluded volume	141590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3emj__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3emj__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Inorganic pyrophosphatase
Molecular weight formula_weight	19629.8 kDa
EC 编号 ec_number	3.6.1.1
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	16189

SMFIKKIKAKANNNEINVIIEIPMNSGPIKYEFDKESGALFVDRFMQTTMSYPCNYGFIPDTLSNDGDPVDVLVVAHHPVVPGSVIKCRAIGVLMMEDESGLDEKIIAVPTSKLDITFDHIKELDDLCEMLKKRIVHFFEHYKDLEKGKWVKVTGWGDKVKAETLIKEGIDRN

Source Source

Source organism organism	Rickettsia prowazekii
NCBI taxonomy ID ncbi_taxonomy_id	782
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	420

▼

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3emjA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3emjB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3emjC00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3emjD00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3emjE00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3emjF00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3emjG00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3emjH00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3emjI00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3emjJ00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3emjK00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3emjL00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

▶

Unit-cell length a length_a	80.960 Å
Unit-cell length b length_b	107.350 Å
Unit-cell length c length_c	128.420 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.05 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2293
R_work r_work	0.2273
R_free r_free	0.2666

2.2 A crystal structure of inorganic pyrophosphatase from rickettsia prowazekii (p21 form)

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

3emj__assembly_2__model_1

3emj__assembly_2__model_1 | I(q)

3emj__assembly_2__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 (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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

2.2 A crystal structure of inorganic pyrophosphatase from rickettsia prowazekii (p21 form)

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

3emj__assembly_2__model_1

3emj__assembly_2__model_1 | I(q)

3emj__assembly_2__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 (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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)