SAXSdb — 9ub8

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1. Structure Basics

entry_id	9ub8
deposition_date	2025-04-02
title	Structure of glycosylphosphatidylinositol transamidase,state 2
keywords	GPI achoring, Transamidase, Membrane protein; MEMBRANE 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	64.39 Å
rg_electron	64.48 Å
i0	2485110000.00
molecular_weight	449240.0 kDa
excluded_volume	572990 Å³
envelope_volume	876960 Å³
shell_volume	115060 Å³
envelope_diameter	230.4 Å
shell_rg	63.64 Å
envelope_rg	63.30 Å
shape_rg	64.49 Å
total_rg	64.43 Å
total_atoms	31758
n_residues	3976
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	233.9 Å
rg_real	64.66 Å
rg_real_error	2.82 Å
i0_real	2.4850e+09
i0_real_error	5.5410e+07
rg_reciprocal	64.12 Å
i0_reciprocal	2483000000.0000
total_estimate	0.8520
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	78.0 Å
skewness	0.405
kurtosis	-0.291
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0000
highest_alpha	176900000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.744

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	GPI transamidase component GAA1
formula_weight	69279.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,E
atom_count	31758

MALLEKLHRRIVDMGLVPRIIALLPVISMLCALFGFISIAILPMDGQYRRTYISENALMPSQAYSYFRESEWNILRGYRSQIKEMVNMTSMERNNLMGSWLQEFGTKTAIYENEQYGETLYGVMHAPRGDGTEAMVLAVPWFNSDDEFNIGGAALGVSLARFFSRWPVWSKNIIVVFSENPRAALRSWVEAYHTSLDLTGGSIEAAVVLDYSSTEDFFEYVEISYDGLNGELPNLDLVNIAISITEHEGMKVSLHGLPSDQLTNNNFWSRLKILCLGIRDWALSGVKKPHGNEAFSGWRIQSVTLKAHGNSGHDITTFGRIPEAMFRSINNLLEKFHQSFFFYLLLAPRQFVSISSYLPSAVALSIAFAISSLNAFINNAYANISLFSEYNLVALLVWFVSLVISFVVSQAFLLIPSSGLLMTISMASCFLPLILSRKIHISEPLSYRLKNVAFLYFSLVSTSLLMINFAMALLIGTLAFPMTFVKTIVESSSEHEVTTQSSNPIKTEPKDEIELVENHMDTTPATPQQQKQKLKNLVLLILTNPFISITLFGLFFDDEFHGFDIINKLVSAWLDLKCWSWFVLCIGWLPCWLLILASSFESKSVVVRSKEKQS

Source

organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
common_name	;Baker's yeast ;
ncbi_taxonomy_id	559292
host_organism	Homo sapiens

Entity 2 polymer

description	GPI transamidase component GAB1
formula_weight	44768.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F

MDSTALKVALGCIAIRLAVNSLFPSLQQQLDQSVEFSTPVTSFRSLQEGIYLLRNNIQVYNHGVVHHPPILIFFLSLFNSDRLISLIYALIDGLIAYQLTEVTKAFKNLKLKVWLPGLLYAVNPLTLLSCISRSSIIFTNFAISSSLYCILAEGNVLLSSVMISISGYLSVYPILLLIPLLGMLKSWRQRILSAIVSILSLLILLLFSYSILGSQSWSFLTQVYGSIITFEKVFPNLGLWWYFFIEMFDTFIPFFKAVFNIFIAVFITPFTLRYHKQPFYAFILCIGWIVLTKPYPSLGDAGFFFSFLPFFTPLFGYLRYPIISALLFLHAIVLAPIFYHLWVVLGSGNSNFFYAISLVYALAIASILVDLNWAMLRIEYDNGIPNFKLKVTQI

Source

organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
common_name	;Baker's yeast ;
ncbi_taxonomy_id	559292
host_organism	Homo sapiens

Entity 3 polymer

description	GPI transamidase component GPI17
formula_weight	60862.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,G

MSNANLRKWVGFCFVAIYLFLGVPLWYKLTTVYRASLPINYIESLQNNKFQDIHLVIPVYVKSDTYRFPDVHDAIQVQVNHLLNSQEQRVPWSLQVLPYNETIEQMESEGNQFHVVTLKLDEFIGYSSAYDTKETLVYYDDAAVLSNDLPFFVAQTLVEHTFQLEWTHLNKTCEGVSTNNDVAISYDPNIHLSVTLLSGDGNPVAWEIEPTLTDYFSPFRKFLSPLVNFTVDSSIVYHNDLNLHSLNGSCTSVTWFDLSHTIDLSELSSMAYYPEDSALNLAIVFPSASSSPDGLAFINGTRISDEITTLDWNSYLVPQWGVIIINKMPLKPNSVISEDYLEPMMYRFATDIFQLLGLTEGSQDLLSPYITIDSFKRLTILQNLDKATETLWSLVKLTQQFQGMSIPREVSDNVIEALDLRLQIIDLLNDPGKGGDIVWNNALHLSNELVKLCEKAFFNGEMVQQNFFPQEHMIAVYLPLLGPISAVMFFGFYNVMKEKNQKSKKNGTEREVAKEKLELKEAQKLHAIDGEDEL

Source

organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
common_name	;Baker's yeast ;
ncbi_taxonomy_id	559292
host_organism	Homo sapiens

Entity 4 polymer

description	GPI transamidase component GPI16
formula_weight	68836.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,H

MILTLAYFMLGTLLLGVFAEDTVSQIGINDSLWYPYDEALVLKPLPNNDLLLSFAFQLQSEPFDPAVSSMSYDAYEHYTTFPRAIPPLLESTATRQFHLRFTRGFWDALSWGQLPHAGKEAGASGVELWSQVQAMDQEQAFHNWKKLSNSLSGLFCSSLNFIDESRTTFPRRSYASDIGAPLFNSTEKLYLMRASLPNEPICTENLTPFIKLLPTRGKSGLTSLLDGHKLFDSLWNSISLDIATICSEDEDALCHYEMDARIEMVTHVPSALARGERPIPKPLDGNTLRCDTDKPFDSYQCFPLPEPSQTHFKLSQLFARPINNGNLFANRPTRICAEVDRSTWTAFLSVDDTIFSTHDNCFDLSNDQNEGGSGYDFILESTDTTKVTPIVPVPIHVSRSLTGNGQDRGGMRIVFHNDNDTPVKLIYFESLPWFMRVYLSSLQITSTTSPQLQENDIILDKYYLQAADRKRPGHLEFTMLIPANTDIVMTYQFDKALLQFAEYPPDANHGFEIDAAVITVLSLESSSSLYEMRTSTLLLSLSTPDFSMPYNVIILTSTIMGLIFGMLYNLMVKRMVTVEEADKITLQSGLKYKLLKLKEKFLGKKKTKTD

Source

organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
common_name	;Baker's yeast ;
ncbi_taxonomy_id	559292
host_organism	Homo sapiens

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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	4.41 Å
resolution_method	—
num_particles	29585

fit	/app/data/saxs_computation/ub/9ub8/9ub8.fit
pddf	/app/data/pr_computation/ub/9ub8/9ub8.pr.out
profile	/app/data/saxs_computation/ub/9ub8/9ub8.dat

Structure of glycosylphosphatidylinositol transamidase,state 2

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)