SAXSdb — 1qy7

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

Nitrogen regulatory protein P-II

Synechococcus elongatus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	SULFATE ION × 6 NICKEL (II) ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLNB_SYNP7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–112； UniProt 1–112 Author chain B； PDBConstruct 1–112； UniProt 1–112 Author chain C； PDBConstruct 1–112； UniProt 1–112

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	1qy7
Deposition date deposition_date	2003-09-09
Structure title title	The structure of the PII protein from the cyanobacteria Synechococcus sp. PCC 7942
Keywords keywords	alpha/beta, Transcription; TRANSCRIPTION
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.

1qy7__assembly_1__model_1

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

Download this curve (.dat)

1qy7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1qy7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.86 Å
Rg (electron density)	21.48 Å
Total Rg	22.17 Å
Atom count	2643
Residues	336
Excluded volume	47529 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1qy7__assembly_1__model_1`	trimeric （3）	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	Nitrogen regulatory protein P-II
Molecular weight formula_weight	12393.3 kDa
Mutation mutation	S49A
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	2775

MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGAEYTVEFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKNADAI

Source Source

Source organism organism	Synechococcus elongatus
NCBI taxonomy ID ncbi_taxonomy_id	1140
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	6

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	132

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1qy7a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.1 — Prokaryotic signal transducing protein

Domain ID domain_id	d1qy7b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.1 — Prokaryotic signal transducing protein

Domain ID domain_id	d1qy7c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.1 — Prokaryotic signal transducing protein

CATH v4.4 (3 domains)

Domain ID domain_id	1qy7A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1qy7B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1qy7C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

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Unit-cell length a length_a	109.700 Å
Unit-cell length b length_b	109.700 Å
Unit-cell length c length_c	109.680 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	48

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	0.1990
R_free r_free	0.2270

The structure of the PII protein from the cyanobacteria Synechococcus sp. PCC 7942

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

Nitrogen regulatory protein P-II

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

1qy7__assembly_1__model_1

1qy7__assembly_1__model_1 | I(q)

1qy7__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

The structure of the PII protein from the cyanobacteria Synechococcus sp. PCC 7942

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

Nitrogen regulatory protein P-II

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

1qy7__assembly_1__model_1

1qy7__assembly_1__model_1 | I(q)

1qy7__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)