SAXSdb — 2bde

▼

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

;cytosolic IMP-GMP specific 5'-nucleotidase ;

Legionella pneumophila

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 8 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 4 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZZB6_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–459； UniProt 1–459

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	2bde
Deposition date deposition_date	2005-10-20
Structure title title	Crystal Structure of the cytosolic IMP-GMP specific 5'-nucleotidase (lpg0095) from Legionella pneumophila, Northeast Structural Genomics Target LgR1
Keywords keywords	;alpha beta protein, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, DNA BINDING PROTEIN ;; DNA BINDING PROTEIN
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.

2bde__assembly_1__model_1

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

Download this curve (.dat)

2bde__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bde__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.78 Å
Rg (electron density)	37.92 Å
Total Rg	38.53 Å
Atom count	15072
Residues	1800
Excluded volume	270080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bde__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2bde__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2bde__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Description description	;cytosolic IMP-GMP specific 5'-nucleotidase ;
Molecular weight formula_weight	55158.5 kDa
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	3839

MDTHKVFVNRIINMRKIKLIGLDMDHTLIRYNSKNFESLVYDLVKERLAESFHYPEEIKKFKFNFDDAIRGLVIDSKNGNILKLSRYGAIRLSYHGTKQISFSDQKKIYRSIYVDLGDPNYMAIDTSFSIAFCILYGQLVDLKDTNPDKMPSYQAIAQDVQYCVDKVHSDGTLKNIIIKNLKKYVIREKEVVEGLKHFIRYGKKIFILTNSEYSYSKLLLDYALSPFLDKGEHWQGLFEFVITLANKPRFFYDNLRFLSVNPENGTMTNVHGPIVPGVYQGGNAKKFTEDLGVGGDEILYIGDHIYGDILRLKKDCNWRTALVVEELGEEIASQIRALPIEKKIGEAMAIKKELEQKYVDLCTRSIDESSQQYDQEIHDLQLQISTVDLQISRLLQEQNSFYNPKWERVFRAGAEESYFAYQVDRFACIYMEKLSDLLEHSPMTYFRANRRLLAHDIDIAAALEHHHHHH

Source Source

Source organism organism	Legionella pneumophila
NCBI taxonomy ID ncbi_taxonomy_id	446
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 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	71

▼

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2bdea1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.23 — 5' nucleotidase-like

CATH v4.4 (2 domains)

Domain ID domain_id	2bdeA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	2bdeA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1160 —

▶

Unit-cell length a length_a	152.540 Å
Unit-cell length b length_b	152.540 Å
Unit-cell length c length_c	188.406 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	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	30.120 Å
R factor r_factor	0.2210
R_work r_work	0.2210
R_free r_free	0.2670

Crystal Structure of the cytosolic IMP-GMP specific 5'-nucleotidase (lpg0095) from Legionella pneumophila, Northeast Structural Genomics Target LgR1

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

;cytosolic IMP-GMP specific 5'-nucleotidase ;

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

2bde__assembly_1__model_1

2bde__assembly_1__model_1 | I(q)

2bde__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 (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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of the cytosolic IMP-GMP specific 5'-nucleotidase (lpg0095) from Legionella pneumophila, Northeast Structural Genomics Target LgR1

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

;cytosolic IMP-GMP specific 5'-nucleotidase ;

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

2bde__assembly_1__model_1

2bde__assembly_1__model_1 | I(q)

2bde__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 (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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)