SAXSdb — 3eeu

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

Probable pyrophosphohydrolase

Bdellovibrio bacteriovorus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	HOLMIUM ATOM × 2 ACETATE ION × 2 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6MPX4_BDEBA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–153； UniProt 1–153 Author chain B； PDBConstruct 1–153； UniProt 1–153

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	3eeu
Deposition date deposition_date	2008-09-05
Structure title title	Structure of the RNA pyrophosphohydrolase BdRppH in complex with Holmium
Keywords keywords	Nudix, RNA pyrophosphohydrolase, 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.

3eeu__assembly_1__model_1

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

Download this curve (.dat)

3eeu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3eeu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.87 Å
Rg (electron density)	19.58 Å
Total Rg	20.46 Å
Atom count	2138
Residues	262
Excluded volume	38283 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3eeu__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	Probable pyrophosphohydrolase
Molecular weight formula_weight	17634.3 kDa
EC 编号 ec_number	3.6.1.-
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	2253

MTDDSAVESKQKKSKIRKGHWIPVVAGFLRKDGKILVGQRPENNSLAGQWEFPGGKIENGETPEEALARELNEELGIEAEVGELKLACTHSYGDVGILILFYEILYWKGEPRAKHHMMLEWIHPEELKHRNIPEANRKILHKIYKALGLEWRK

Source Source

Source organism organism	Bdellovibrio bacteriovorus
NCBI taxonomy ID ncbi_taxonomy_id	959
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	HOLMIUM ATOM
Molecular weight formula_weight	164.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	115

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3eeua_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.113 — Nudix
Superfamily Superfamily superfamily	d.113.1 — Nudix
Family Family family	d.113.1.0 — automated matches

Domain ID domain_id	d3eeub_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.113 — Nudix
Superfamily Superfamily superfamily	d.113.1 — Nudix
Family Family family	d.113.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3eeuA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

Domain ID domain_id	3eeuB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

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Unit-cell length a length_a	70.212 Å
Unit-cell length b length_b	70.212 Å
Unit-cell length c length_c	99.915 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 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	30.400 Å
R factor r_factor	0.2180
R_work r_work	0.2160
R_free r_free	0.2560

Structure of the RNA pyrophosphohydrolase BdRppH in complex with Holmium

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

Probable pyrophosphohydrolase

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

3eeu__assembly_1__model_1

3eeu__assembly_1__model_1 | I(q)

3eeu__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of the RNA pyrophosphohydrolase BdRppH in complex with Holmium

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

Probable pyrophosphohydrolase

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

3eeu__assembly_1__model_1

3eeu__assembly_1__model_1 | I(q)

3eeu__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)