SAXSdb — 9zwk

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1. Structure Basics

entry_id	9zwk
deposition_date	2026-01-03
title	High-resolution cryo-EM structure of KdpFABC in the E1 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	42.06 Å
rg_electron	41.42 Å
i0	321059000.00
molecular_weight	155390.0 kDa
excluded_volume	198500 Å³
envelope_volume	247000 Å³
shell_volume	52533 Å³
envelope_diameter	153.6 Å
shell_rg	43.56 Å
envelope_rg	42.08 Å
shape_rg	41.48 Å
total_rg	41.33 Å
total_atoms	10916
n_residues	1452
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	145.8 Å
rg_real	42.45 Å
rg_real_error	1.46 Å
i0_real	3.2110e+08
i0_real_error	5.5250e+06
rg_reciprocal	42.06 Å
i0_reciprocal	320900000.0000
total_estimate	0.5944
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	38.4 Å
skewness	0.583
kurtosis	-0.227
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	50920000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.734; Stabil: 1.000; Sysdev: 0.046; Positv: 1.000; Valcen: 0.859; Smooth: 0.525

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

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	11017

MAAQGFLLIATFLLVLMVLARPLGSGLARLINDIPLPGTTGVERVLFRALGVSDREMNWKQYLCAILGLNMLGLAVLFFMLLGQHYLPLNPQQLPGLSWDLALNTAVSFVTNTNWQSYSGETTLSYFSQMAGLTVQNFLSAASGIAVIFALIRAFTRQSMSTLGNAWVDLLRITLWVLVPVALLIALFFIQQGALQNFLPYQAVNTVEGAQQLLPMGPVASQEAIKMLGTNGGGFFNANSSHPFENPTALTNFVQMLAIFLIPTALCFAFGEVMGDRRQGRMLLWAMSVIFVICVGVVMWAEVQGNPHLLALGTDSSINMEGKESRFGVLVSSLFAVVTTAASCGAVIAMHDSFTALGGMVPMWLMQIGEVVFGGVGSGLYGMMLFVLLAVFIAGLMIGRTPEYLGKKIDVREMKLTALAILVTPTLVLMGAALAMMTDAGRSAMLNPGPHGFSEVLYAVSSAANNNGSAFAGLSANSPFWNCLLAFCMFVGRFGVIIPVMAIAGSLVSKKSQAASSGTLPTHGPLFVGLLIGTVLLVGALTFIPALALGPVAEYLS

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli

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 K-12
ncbi_taxonomy_id	83333
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 K-12
ncbi_taxonomy_id	83333
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 K-12
ncbi_taxonomy_id	83333
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 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	101

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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	2.340 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.34 Å
resolution_method	—
num_particles	89556

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

High-resolution cryo-EM structure of KdpFABC in the E1 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 (7)

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 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)