SAXSdb — 9pnd

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1. Structure Basics

entry_id	9pnd
deposition_date	2025-07-20
title	In situ microtubule of EpoB-induced regenerating axons
keywords	cytoskeleton, microtubules, neuroregeneration, axon, STRUCTURAL PROTEIN; STRUCTURAL 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	51.84 Å
rg_electron	52.80 Å
i0	592869000.00
molecular_weight	196340.0 kDa
excluded_volume	243380 Å³
envelope_volume	330110 Å³
shell_volume	59070 Å³
envelope_diameter	193.8 Å
shell_rg	46.34 Å
envelope_rg	53.19 Å
shape_rg	52.80 Å
total_rg	52.56 Å
total_atoms	13774
n_residues	1734
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	180.7 Å
rg_real	52.60 Å
rg_real_error	2.47 Å
i0_real	5.9290e+08
i0_real_error	1.4190e+07
rg_reciprocal	51.19 Å
i0_reciprocal	591700000.0000
total_estimate	0.6820
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	36.1 Å
skewness	0.685
kurtosis	-0.319
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	109400000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.386; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.585; Smooth: 0.122

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Tubulin beta-3 chain
formula_weight	50467.5 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D
atom_count	13778

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYVPRAILVDLEPGTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKLATPTYGDLNHLVSATMSGVTTSLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTARGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRGLKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEGEMYEDDDEESEAQGPK

Entity 2 polymer

description	Detyrosinated tubulin alpha-1A chain
formula_weight	50188.4 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE
formula_weight	507.7 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	GUANOSINE-5'-TRIPHOSPHATE
formula_weight	523.2 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	4

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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	3.190 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.19 Å
resolution_method	—
num_particles	118551

fit	/app/data/saxs_computation/pn/9pnd/9pnd.fit
pddf	/app/data/pr_computation/pn/9pnd/9pnd.pr.out
profile	/app/data/saxs_computation/pn/9pnd/9pnd.dat

In situ microtubule of EpoB-induced regenerating axons

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

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)