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9zno

Cryo-EM structure of Hydrogenivirga sp. MraY in complex with APPB

Method: ELECTRON MICROSCOPY D_max: 81.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zno
deposition_date	2025-12-14
title	Cryo-EM structure of Hydrogenivirga sp. MraY in complex with APPB
keywords	polyprenyl-phosphate N-acetylhexosamine phosphate transferase, phosphoglycosyltransferases, membrane protein, TRANSFERASE; TRANSFERASE
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	26.29 Å
rg_electron	25.54 Å
i0	149248000.00
molecular_weight	69428.0 kDa
excluded_volume	69852 Å³
envelope_volume	111060 Å³
shell_volume	34954 Å³
envelope_diameter	84.2 Å
shell_rg	34.11 Å
envelope_rg	25.82 Å
shape_rg	25.56 Å
total_rg	26.20 Å
total_atoms	5312
n_residues	662
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	81.5 Å
rg_real	26.17 Å
rg_real_error	0.47 Å
i0_real	1.4920e+08
i0_real_error	2.0200e+06
rg_reciprocal	26.21 Å
i0_reciprocal	149300000.0000
total_estimate	0.9067
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	31.2 Å
skewness	0.208
kurtosis	-0.458
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	18510000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Phospho-N-acetylmuramoyl-pentapeptide-transferase (MraY)
formula_weight	40962.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5436

HHHHHHMIYHLAILLREHFFAFNVLKYITFRSFTAILLAFFITLILSPTFMKKFAKIQRLFGGYVREYTPEHHESKKYTPTMGGVVIVTVILITSVLLMRLDIRYTWVLVFSTLSFALIGFVDDWIKLKNKKGLSIKAKLAFQMSFALAVSLLIFYWVGLETKLYFPFFKELTVDLGWLYIPFSMFIIVGTANAVNLTDGLDGLAIGPSMTTATAFGVIAYVVGHSKIAQYLGVPHVPYAGEITVFCFAIIGAGLGFLWFNTYPAQVFMGDVGALGLGAALATVSIMTKSEFLLAVAGGVFVFETVTVILQIIYFRATGGKRLFRKAPFHHHLEEKGLDEPKIVVRMWIVSALLAIVSVAMLKLR

Source

organism	Hydrogenivirga sp. 128-5-R1-1
ncbi_taxonomy_id	392423
host_organism	Escherichia coli K-12

Entity 2 non-polymer

description	;4-({(2S,3S)-1-amino-3-{[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-dihydroxyoxolan-2-yl]oxy}-3-[(2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]-1-oxopropan-2-yl}amino)-N-[(4-{4-[4-(trifluoromethoxy)phenoxy]piperidin-1-yl}phenyl)methyl]butanamide (non-preferred name) ;
formula_weight	881.8 kDa
src_method	syn
entity_count	2

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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	2.910 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.91 Å
resolution_method	—
num_particles	107945

fit	/app/data/saxs_computation/zn/9zno/9zno.fit
pddf	/app/data/pr_computation/zn/9zno/9zno.pr.out
profile	/app/data/saxs_computation/zn/9zno/9zno.dat

Cryo-EM structure of Hydrogenivirga sp. MraY in complex with APPB

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)