SAXSdb — 1a6j

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

NITROGEN REGULATORY IIA PROTEIN

Escherichia coli

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–163 Chain B； UniProt 1–163	Not recorded	BME BETA-MERCAPTOETHANOL × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；PROTEIN CRYSTALLIZED WITH THE HANGING DROP SETUP. RESERVOIR CONTAINING 1.8 M AMMONIUM SULPHATE, 1 MM SODIUM AZIDE, 2MM DTT AND 0.1 M BES-NAOH, PH 7.5.	Resolution 2.35 Å R-free 0.251

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	PTSN_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–163； UniProt 1–163 Author chain B； PDBConstruct 1–163； UniProt 1–163

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	1a6j
Deposition date deposition_date	1998-02-25
Structure title title	NITROGEN REGULATORY BACTERIAL PROTEIN IIA-NITROGEN
Keywords keywords	PHOSPHOTRANSFERASE SYSTEM, NITROGEN REGULATION; PHOSPHOTRANSFERASE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.33 Å
Radius of gyration Rg (electron density) rg_electron	20.31 Å
Forward intensity I(0) i0	20415100.00
Molecular weight molecular_weight	34216.0 kDa
Excluded volume excluded_volume	42960 Å³
Envelope volume envelope_volume	50235 Å³
Hydration-shell volume shell_volume	20834 Å³
Envelope diameter envelope_diameter	68.0 Å
Shell Rg shell_rg	26.54 Å
Envelope Rg envelope_rg	20.49 Å
Shape Rg shape_rg	20.30 Å
Total Rg total_rg	21.16 Å
Total atoms total_atoms	2396
Residues n_residues	307
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	67.2 Å
Rg (real space) rg_real	21.30 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	2.0420e+07
I(0) uncertainty (real space) i0_real_error	2.6100e+05
Rg (reciprocal space) rg_reciprocal	21.31 Å
I(0) (reciprocal space) i0_reciprocal	20420000.0000
Solution quality estimate total_estimate	0.8986
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.7 Å
Skewness Skewness skewness	0.320
Kurtosis Kurtosis kurtosis	-0.392
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5204000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	NITROGEN REGULATORY IIA PROTEIN
Molecular weight formula_weight	17981.5 kDa
EC 编号 ec_number	2.7.1.69
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	2461

MTNNDTTLQLSSVLNRECTRSRVHCQSKKRALEIISELAAKQLSLPPQVVFEAILTREKMGSTGIGNGIAIPHGKLEEDTLRAVGVFVQLETPIAFDAIDNQPVDLLFALLVPADQTKTHLHTLSLVAKRLADKTICRRLRAAQSDEELYQIITDTEGTPDEA

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	65

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1a6ja_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.112 — Phoshotransferase/anion transport protein
Superfamily Superfamily superfamily	d.112.1 — Phoshotransferase/anion transport protein
Family Family family	d.112.1.1 — IIA domain of mannitol-specific and ntr phosphotransferase EII

Domain ID domain_id	d1a6jb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.112 — Phoshotransferase/anion transport protein
Superfamily Superfamily superfamily	d.112.1 — Phoshotransferase/anion transport protein
Family Family family	d.112.1.1 — IIA domain of mannitol-specific and ntr phosphotransferase EII

CATH v4.4 (2 domains)

Domain ID domain_id	1a6jA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	930 — Mannitol-specific EII; Chain A
Homologous superfamily homologous superfamily	10 — Mannitol-specific EII; Chain A

Domain ID domain_id	1a6jB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	930 — Mannitol-specific EII; Chain A
Homologous superfamily homologous superfamily	10 — Mannitol-specific EII; Chain A

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8. Citations (1)

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Unit-cell length a length_a	107.900 Å
Unit-cell length b length_b	107.900 Å
Unit-cell length c length_c	64.300 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	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2510

fit	/app/data/saxs_computation/a6/1a6j/1a6j.fit
pddf	/app/data/pr_computation/a6/1a6j/1a6j.pr.out
profile	/app/data/saxs_computation/a6/1a6j/1a6j.dat

NITROGEN REGULATORY BACTERIAL PROTEIN IIA-NITROGEN

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

NITROGEN REGULATORY IIA PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction