SAXSdb — 2qjo

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

Bifunctional NMN adenylyltransferase/Nudix hydrolase

Synechocystis sp.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	SULFATE ION × 8 ADENOSINE-5-DIPHOSPHORIBOSE × 6 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 6 PYROPHOSPHATE 2- × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NADM_SYNY3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–341； UniProt 1–339 Author chain B； PDBConstruct 3–341； UniProt 1–339 Author chain C； PDBConstruct 3–341； UniProt 1–339

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	2qjo
Deposition date deposition_date	2007-07-08
Structure title title	crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp.
Keywords keywords	two individual domains, TRANSFERASE, HYDROLASE; TRANSFERASE, 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.

2qjo__assembly_1__model_1

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

Download this curve (.dat)

2qjo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qjo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.95 Å
Rg (electron density)	43.23 Å
Total Rg	43.61 Å
Atom count	16618
Residues	1990
Excluded volume	294740 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qjo__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 (6)

Entity 1 Entity 1 polymer

Description description	Bifunctional NMN adenylyltransferase/Nudix hydrolase
Molecular weight formula_weight	38790.3 kDa
EC 编号 ec_number	2.7.7.1, 3.6.1.-
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	8648

DPMQTKYQYGIYIGRFQPFHLGHLRTLNLALEKAEQVIIILGSHRVAADTRNPWRSPERMAMIEACLSPQILKRVHFLTVRDWLYSDNLWLAAVQQQVLKITGGSNSVVVLGHRKDASSYYLNLFPQWDYLETGHYPDFSSTAIRGAYFEGKEGDYLDKVPPAIADYLQTFQKSERYIALCDEYQFLQAYKQAWATAPYAPTFITTDAVVVQAGHVLMVRRQAKPGLGLIALPGGFIKQNETLVEGMLRELKEETRLKVPLPVLRGSIVDSHVFDAPGRSLRGRTITHAYFIQLPGGELPAVKGGDDAQKAWWMSLADLYAQEEQIYEDHFQIIQHFVSKV

Source Source

Source organism organism	Synechocystis sp.
NCBI taxonomy ID ncbi_taxonomy_id	1148
Host organism host_organism	Escherichia coli BL21

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	4

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5-DIPHOSPHORIBOSE
Molecular weight formula_weight	559.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	PYROPHOSPHATE 2-
Molecular weight formula_weight	176.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	313

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2qjoA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	2qjoA02
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	2qjoB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	2qjoB02
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	2qjoC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	2qjoC02
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	201.540 Å
Unit-cell length b length_b	201.540 Å
Unit-cell length c length_c	98.695 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	18

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	43.480 Å
R factor r_factor	0.1957
R_work r_work	0.1940
R_free r_free	0.2277

crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp.

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

Bifunctional NMN adenylyltransferase/Nudix hydrolase

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

2qjo__assembly_1__model_1

2qjo__assembly_1__model_1 | I(q)

2qjo__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp.

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

Bifunctional NMN adenylyltransferase/Nudix hydrolase

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

2qjo__assembly_1__model_1

2qjo__assembly_1__model_1 | I(q)

2qjo__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)