SAXSdb — 9qq6

▼

1. Structure Basics

entry_id	9qq6
deposition_date	2025-03-31
title	Structure of the Azotobacter vinelandii NifL-NifA complex
keywords	biological nitrogen fixation, transcriptional regulation, sustainable agriculture, GENE REGULATION; GENE REGULATION
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	50.84 Å
rg_electron	51.96 Å
i0	312667000.00
molecular_weight	141820.0 kDa
excluded_volume	176210 Å³
envelope_volume	245940 Å³
shell_volume	43853 Å³
envelope_diameter	180.5 Å
shell_rg	46.85 Å
envelope_rg	51.69 Å
shape_rg	52.01 Å
total_rg	51.58 Å
total_atoms	19911
n_residues	1243
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	167.9 Å
rg_real	51.53 Å
rg_real_error	2.31 Å
i0_real	3.1270e+08
i0_real_error	6.2670e+06
rg_reciprocal	50.25 Å
i0_reciprocal	312100000.0000
total_estimate	0.6700
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	37.9 Å
skewness	0.600
kurtosis	-0.594
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	12390000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.457; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.323; Smooth: 0.014

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	histidine kinase
formula_weight	59897.2 kDa
ec_number	2.7.13.3
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	19911

MASWSHPQFEKGADDDDKVTPANPTLSNEPQAPHAESDELLPEIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVLVNRRKDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSELHELEQRVNNQRLMIEAVVNAAPAAMVVLDRQHRVMLSNPSFCRLARDLVEDGSSESLVALLRENLAAPFETLENQGSAFSGKEISFDLGGRSPRWLSCHGRAIHIENEQAHVFFAPTEERYLLLTINDISELRQKQQDSRLNALKALMAEEELLEGMRETFNAAIHRLQGPVNLISAAMRMLERRLGDKAGNDPVLSAMREASTAGMEALENLSGSIPVRMAESKMPVNLNQLIREVITLCTDQLLAQGIVVDWQPALRLPWVMGGESSLRSMIKHLVDNAIESMSQNQVSRRELFISTRVENHLVRMEITDSGPGIPPDLVLKVFEPFFSTKPPHRVGRGMGLPVVQEIVAKHAGMVHVDTDYREGCRIVVELPFSAST

Source

organism	Azotobacter vinelandii DJ
ncbi_taxonomy_id	322710
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Nif-specific regulatory protein
formula_weight	58979.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MNATIPQRSAKQNPVELYDLQLQALASIARTLSREQQIDELLEQVLAVLHNDLGLLHGLVTISDPEHGALQIGAIHTDSEAVAQACEGVRYRSGEGVIGNVLKHGNSVVLGRISADPRFLDRLALYDLEMPFIAVPIKNPEGNTIGVLAAQPDCRADEHMPARTRLLEIVANLLAQTVRLVVNIEDGREAADERDELRREVRGKYGFENMVVGHTPTMRRVFDQIRRVAKWNSTVLVLGESGTGKELIASAIHYNSPRAHRPFVRLNCAALPETLLESELFGHEKGAFTGAVKQRKGRFEQADGGTLFLDEIGEISPMFQAKLLRVLQEGEFERVGGNQTVRVNVRIVAATNRDLESEVEKGKFREDLYYRLNVMAIRIPPLRERTADIPELAEFLLGKIGRQQGRPLTVTDSAIRLLMSHRWPGNVRELENCLERSAIMSEDGTITRDVVSLTGVDNESPPLAAPLPEVNLADETLDDRERVIAALEQAGWVQAKAARLLGMTPRQIAYRIQTLNIHMRKIHHHHHH

Source

organism	Azotobacter vinelandii DJ
ncbi_taxonomy_id	322710
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	3

▶

6. Citations (1)

▶

length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	6.45 Å
resolution_method	—
num_particles	209009

fit	/app/data/saxs_computation/qq/9qq6/9qq6.fit
pddf	/app/data/pr_computation/qq/9qq6/9qq6.pr.out
profile	/app/data/saxs_computation/qq/9qq6/9qq6.dat

Structure of the Azotobacter vinelandii NifL-NifA complex

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)