SAXSdb — 9pzm

▼

1. Structure Basics

entry_id	9pzm
deposition_date	2025-08-11
title	Augmin V junction with NEDD1 (WD)
keywords	Microtubule nucleator, PLANT PROTEIN; PLANT PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	65.86 Å
rg_electron	68.01 Å
i0	597563000.00
molecular_weight	200370.0 kDa
excluded_volume	249670 Å³
envelope_volume	405960 Å³
shell_volume	57722 Å³
envelope_diameter	255.8 Å
shell_rg	53.31 Å
envelope_rg	68.36 Å
shape_rg	68.04 Å
total_rg	67.49 Å
total_atoms	14092
n_residues	1785
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	227.0 Å
rg_real	67.18 Å
rg_real_error	2.78 Å
i0_real	5.9720e+08
i0_real_error	1.4090e+07
rg_reciprocal	64.58 Å
i0_reciprocal	594700000.0000
total_estimate	0.5135
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	37.8 Å
skewness	0.536
kurtosis	-0.338
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0013
highest_alpha	15330000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.568; Stabil: 0.998; Sysdev: 0.013; Positv: 1.000; Valcen: 0.508; Smooth: 0.427

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (7)

Entity 1 polymer

description	AUGMIN subunit 2
formula_weight	16952.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	14092

SDALSIASDLGFAVAPPPSQEELQSFASSNGERGDDLIRVLRELSVVQRKIADLQVELQGRKDDKNVAHLTHVGEMQKKIETLSRITQILKDVIQNKDRIIARLQQPYSLDCIPVEAEYQKQFSELLMKAASDYGALTASVSDFQWSQSMQG

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Escherichia coli

Entity 2 polymer

description	AUGMIN subunit 3
formula_weight	69809.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MSSARLCSLVAELGYEGAGKLDPDSFEWPFQYDDARPILDWICSSLRPSNVLSLAELSLYEQFQRDGKLLEGDDLDQAYDSISAFSSRRNNQEAVFGAEESIKEVRDATLAHKAEALELQRQLRRLQTQYDLLTGQSSALIQGRRARVAATSAVSGQITAIEDSLSARNLQMNGVLGRLASTSQELAHYHSGEEDGIYLAYSDFHAYLAGDSACTKELNQWFAKQLDTGPYRLVAEEGKSKCSWVSLDDTSNMLRDLEKSQHQRVAELQRLRSIFGTSERQWIEAQVENAKQQAILLTLKSQVTSVEAHIHFDLHSLRRKHADLVEEISTLYQKEEKLLSETIPELCWELAQLQDTYILQGDYDLKVMRQELYISKQKVFINHLVNQLARHQFLKLACQLEKKNMLGAFSLLKVIESELQGYLSATRSRVGRCSALIQAASDVQEQGAVDDRDSFLHGVRDLLSIHSNTQAGLSTYVSAPAIIQQIVALQSDLSSLQSDLENSLPDDRNRCINELCTHIQNLQQLLFASSTTAQPILTPWPLMKELDEMGKINSKLSTAVEEVTLEHRNKREIVKHHAKDVELQRRVFVDFFCNPERLRNQVRELNALVRARQASSS

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Escherichia coli

Entity 3 polymer

description	AUGMIN subunit 5
formula_weight	87231.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MQSLSSSAPTPEAILEWLQKEMGYRQLGPYNGSSKSHVPSIDAIRKICRGNMIPIWNFLINRVKSEKTVERIRRNITVHGGSSNASIGSSVNPGKEESKSKGRRKDKTVTGESSSYAEDREAALQERELAAKEVERLRNIVRRQRKDLKARMLEVSREEAERKRMLDERANYRHKQALLEAYDQQCDEATRIFAEYHKRLQVYVNQANDAQRSVNSSNEVLSSLSANSEREAVYSTVKGTKSADDVILMETTRERNIRIVCDLLASRMIERIRNSFPAYEGNGICSLPELETAKLGFEYDGEITDEMKTVIVNSLRGPPLLLQAIAAYTLRIKTLISREMEKIDVRADAEMLRYKFENNRVTDNSSSDVSSPSNNQLLERQKAHVQQFLATEDALNKAAEARDLCHKFINRLHGSADTATHSFVGGTTQSGSNLRQFELDVWGKEREAAGLRASLNTLLSEIQRLNKLCAERKEAEDSLKKKWKKIEEFDARRSELETIYTTLLKANMDAVAFWNQQPLAAREYASATVIPASEVVVDISNSAKDFIEKEVSAFFQSPDNSLYMLPATPQGLLESMGANGSTGPEAVAYAEKNAALLTARAGARDPSAIPSICRISAALQYPAGLEGSDASLASVLESLEFCLRVRGSEACVLEDLAKAIDLVHIRQDLVESGHSLLDHAFRAQQKYERTTNYCLDLASEQENTISDQWLPELRTAVQNAQASSEHCKYVRGLLDEWWEQPASTVVDWVTVDGQSVAAWQNHVKQLLAFYDKESLRT

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Escherichia coli

Entity 4 polymer

description	AUGMIN subunit 6
formula_weight	36708.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MTMDREKERELELESAMYTNCLLLGLDPNVIGLGASNGTPRVGLFRHSNPKLGEQLLYFILSSLRGPAQSSKDFDKVWPIFDSAQSRDFRKVVQAIISELESQGALPRSNSRVSSLATCCGPRFVELLWQLSLHALREVHRRTFPADVASNPLPSSLTDVSFSHAATLLPVTKARIVLERRRFLKNAETAVQRQAMWSNLAHEMTAEFRGLCAEEAYLQQELEKLNDLRNKVKQEGEVWDDLVSSSSQNSHLVSKATRLWDSIMARKGQHEVLASGPIEDLIAHREHRYRISGSALLAAMDQSSQVPRAELLSAHSDDSASLADDKEL

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Escherichia coli

Entity 5 polymer

description	AUGMIN subunit 7
formula_weight	37047.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MAAKQMEEIQKKLRLLSYPRANAPAQSLLFAGMERYALLEWLFFKLLGDKSPFSQQNLQGDAGVRDEETVRIQYLAEIAKFLGITPTVDIEAIQGHGTYEDRMEMLRNIVDLVEASLFSDNQEWSIDEQVAKDIQLIDAIAERQSLIFSEECKLFPADVQIQSIYPLPDVSELETKLSEQAKILSNLQQKVDDLAAKHAYNPDEEYTEVESQLRARLESFLETARAFNTIYTKEIRPWTHMMEVPQLHGFGPAANRLLEAYNMLLKFLGNLKNLRDSHAALSIGSSGTVAGEPSSVTRIVSDCEAALTVLNRDLGILSASIAREQGERL

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Escherichia coli

Entity 6 polymer

description	AUGMIN subunit 8
formula_weight	18658.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

EDVHQLRLLHNRYLQWRFAIARAESVMYIQRLTSEETLFNVWHAISELQDHVTRQRIGLQQLKLEIKLNSLLNDQMVSLEDWATLERDHVSSLVGAISDLEANTLRLPATGGTKADTESLKAAMSSALDVMQAMGSSIWSLLSKVEEMNIMVTELAVVVTKESSM

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Escherichia coli

Entity 7 polymer

description	Protein NEDD1
formula_weight	33256.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

WRLLAASGGDTVKLFDVSADSGDPCVLSYTPSPGCAVNSVKWNHTNLVVASTGEDKKISLWRKNGQSLGTVPVTGKDGGDSAEECLSAISFSKKGSRYICSGGTGQIVKIWDLQRKLCIKKLKGHTSTITGVMYNCKDEHLASVSVGGDLIVHNLASGARATELKDPNGQVLRLLDYSRSSRHLLVTAGDDGTVHLWDTTGRSPKMSWLKQHSAPTAGVCFSPSNEKIIASVGMDKKLYTYDSGSRRSSSCIAYEAPFSSLAFGDNGYILVAGTSNGRVVFYDIRGKPQPVTVLHAFSNSEDVTSLSWQT

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Trichoplusia ni

▶

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	triclinic

resolution	8.00 Å
resolution_method	—
num_particles	49000

fit	/app/data/saxs_computation/pz/9pzm/9pzm.fit
pddf	/app/data/pr_computation/pz/9pzm/9pzm.pr.out
profile	/app/data/saxs_computation/pz/9pzm/9pzm.dat

Augmin V junction with NEDD1 (WD)

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)