SAXSdb — 9zwl

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1. Structure Basics

entry_id	9zwl
deposition_date	2026-01-03
title	High-resolution cryo-EM structure of KdpFABC in the E1-ATP state in lipid nanodisc
keywords	P-type ATPase potassium channel transporter pump, TRANSPORT PROTEIN; TRANSPORT PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

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

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2. SAXS Parameters (CRYSOL)

rg_guinier	42.07 Å
rg_electron	41.40 Å
i0	327721000.00
molecular_weight	156330.0 kDa
excluded_volume	199420 Å³
envelope_volume	247130 Å³
shell_volume	52428 Å³
envelope_diameter	153.7 Å
shell_rg	43.56 Å
envelope_rg	42.28 Å
shape_rg	41.46 Å
total_rg	41.33 Å
total_atoms	10977
n_residues	1455
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

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3. P(r) Analysis (GNOM)

dmax	146.2 Å
rg_real	42.45 Å
rg_real_error	1.41 Å
i0_real	3.2770e+08
i0_real_error	5.5930e+06
rg_reciprocal	42.08 Å
i0_reciprocal	327600000.0000
total_estimate	0.8190
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	38.5 Å
skewness	0.569
kurtosis	-0.259
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	48350000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.736; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.856; Smooth: 0.579

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Potassium-transporting ATPase potassium-binding subunit
formula_weight	59218.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	11097

MAAQGFLLIATFLLVLMVLARPLGSGLARLINDIPLPGTTGVERVLFRALGVSDREMNWKQYLCAILGLNMLGLAVLFFMLLGQHYLPLNPQQLPGLSWDLALNTAVSFVTNTNWQSYSGETTLSYFSQMAGLTVQNFLSAASGIAVIFALIRAFTRQSMSTLGNAWVDLLRITLWVLVPVALLIALFFIQQGALQNFLPYQAVNTVEGAQQLLPMGPVASQEAIKMLGTNGGGFFNANSSHPFENPTALTNFVQMLAIFLIPTALCFAFGEVMGDRRQGRMLLWAMSVIFVICVGVVMWAEVQGNPHLLALGTDSSINMEGKESRFGVLVSSLFAVVTTAASCGAVIAMHDSFTALGGMVPMWLMQIGEVVFGGVGSGLYGMMLFVLLAVFIAGLMIGRTPEYLGKKIDVREMKLTALAILVTPTLVLMGAALAMMTDAGRSAMLNPGPHGFSEVLYAVSSAANNNGSAFAGLSANSPFWNCLLAFCMFVGRFGVIIPVMAIAGSLVSKKSQAASSGTLPTHGPLFVGLLIGTVLLVGALTFIPALALGPVAEYLS

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli K-12

Entity 2 polymer

description	Potassium-transporting ATPase ATP-binding subunit
formula_weight	72267.9 kDa
ec_number	7.2.2.6
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MSRKQLALFEPTLVVQALKEAVKKLNPQAQWRNPVMFIVWIGSLLTTCISIAMASGAMPGNALFSAAISGWLWITVLFANFAEALAEGRSKAQANSLKGVKKTAFARKLREPKYGAAADKVPADQLRKGDIVLVEAGDIIPCDGEVIEGGASVDESAITGESAPVIRESGGDFASVTGGTRILSDWLVIECSVNPGETFLDRMIAMVEGAQRRKTPNEIALTILLIALTIVFLLATATLWPFSAWGGNAVSVTVLVALLVCLIPTTIGGLLSAIGVAGMSRMLGANVIATSGRAVEAAGDVDVLLLDKTGTITLGNRQASEFIPAQGVDEKTLADAAQLASLADETPEGRSIVILAKQRFNLRERDVQSLHATFVPFTAQSRMSGINIDNRMIRKGSVDAIRRHVEANGGHFPTDVDQKVDQVARQGATPLVVVEGSRVLGVIALKDIVKGGIKERFAQLRKMGIKTVMITGDNRLTAAAIAAEAGVDDFLAEATPEAKLALIRQYQAEGRLVAMTGDGTNDAPALAQADVAVAMNSGTQAAKEAGNMVDLDSNPTKLIEVVHIGKQMLMTRGSLTTFSIANDVAKYFAIIPAAFAATYPQLNALNIMCLHSPDSAILSAVIFNALIIVFLIPLALKGVSYKPLTASAMLRRNLWIYGLGGLLVPFIGIKVIDLLLTVCGLV

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli K-12

Entity 3 polymer

description	Potassium-transporting ATPase KdpC subunit
formula_weight	22299.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MSGLRPALSTFIFLLLITGGVYPLLTTVLGQWWFPWQANGSLIREGDTVRGSALIGQNFTGNGYFHGRPSATAEMPYNPQASGGSNLAVSNPELDKLIAARVAALRAANPDASASVPVELVTASASGLDNNITPQAAAWQIPRVAKARNLSVEQLTQLIAKYSQQPLVKYIGQPVVNIVELNLALDKLDEGTGLVPRGSSHHHHHHHH

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli K-12

Entity 4 polymer

description	Potassium-transporting ATPase KdpF subunit
formula_weight	3071.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MSAGVITGVLLVFLLLGYLVYALINAEAF

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli K-12

Entity 5 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	(2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate
formula_weight	718.0 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	120

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6. Citations (1)

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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	2.280 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

fit	/app/data/saxs_computation/zw/9zwl/9zwl.fit
pddf	/app/data/pr_computation/zw/9zwl/9zwl.pr.out
profile	/app/data/saxs_computation/zw/9zwl/9zwl.dat

High-resolution cryo-EM structure of KdpFABC in the E1-ATP state in lipid nanodisc

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

Refinement

EM 3D

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

resolution	2.28 Å
resolution_method	—
num_particles	270688