SAXSdb — 9vrb

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1. Structure Basics

entry_id	9vrb
deposition_date	2025-07-06
title	Cryo-EM structure of ATP-bound Oryza sativa MRP5 with E1424Q mutation
keywords	ABC-type transporter, Monomer, 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	35.87 Å
rg_electron	36.25 Å
i0	265401000.00
molecular_weight	136060.0 kDa
excluded_volume	172120 Å³
envelope_volume	208210 Å³
shell_volume	49058 Å³
envelope_diameter	130.0 Å
shell_rg	41.45 Å
envelope_rg	36.45 Å
shape_rg	36.26 Å
total_rg	36.56 Å
total_atoms	9556
n_residues	1212
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	123.0 Å
rg_real	36.14 Å
rg_real_error	0.90 Å
i0_real	2.6540e+08
i0_real_error	5.0770e+06
rg_reciprocal	35.98 Å
i0_reciprocal	265400000.0000
total_estimate	0.8326
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	36.3 Å
skewness	0.591
kurtosis	-0.119
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	86360000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.721; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.904; Smooth: 0.752

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	ABC transporter C family member 13
formula_weight	166320.9 kDa
ec_number	7.-.-.-
mutation	E1424Q
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9556

MPHFPNLPLPEAAAAAAHAALLALALLLLLLRSARALASRCASCLKTAPRRAAAVDGGLAAASSVGAWYRAALACCGYALLAQVAALSYEVAVAGSHVAVEALLLPAVQALAWAALLALAMQARAVGWGRFPVLVRVWWVVSFVLCVGIAYDDTRHLMGDDDDDEVDYAHMVANFASAPALGFLCLVGVMGSTGVELEFTDDDSSVHEPLLLGGQRRDADEEPGCLRVTPYGDAGIVSLATLSWLSPLLSVGAQRPLELADIPLMAHKDRAKSCYKAMSSHYERQRMERPGSEPSLAWAILKSFWREAAINGAFAAVNTIVSYVGPYLISYFVDYLSGKIEFPHEGYILASVFFVAKLLETLTARQWYLGVDVMGIHVKSGLTAMVYRKGLRLSNSSRQSHTSGEIVNYMAVDVQRVGDYAWYFHDIWMLPLQIILALAILYKNVGIAMVSTLVATVLSIAASVPVAKLQEHYQDKLMASKDERMRKTSECLKNMRILKLQAWEDRYRLKLEEMRNVECKWLRWALYSQAAVTFVFWSSPIFVAVITFGTCILLGGELTAGGVLSALATFRILQEPLRNFPDLISMIAQTRVSLDRLSHFLQQEELPDDATITVPHGSTDKAININDATFSWNPSSPTPTLSGINLSVVRGMRVAVCGVIGSGKSSLLSSILGEIPKLCGQVRISGSAAYVPQTAWIQSGNIEENILFGSPMDKQRYKRVIEACSLKKDLQLLQYGDQTIIGDRGINLSGGQKQRVQLARALYQDADIYLLDDPFSAVDAHTGSELFREYILTALASKTVIYVTHQIEFLPAADLILVLKDGHITQAGKYDDLLQAGTDFNALVCAHKEAIETMEFSEDSDEDTVSSVPIKRLTPSVSNIDNLKNKVSNNEKPSSTRGIKEKKKKPEERKKKRSVQEEERERGRVSLQVYLSYMGEAYKGTLIPLIILAQTMFQVLQIASNWWMAWANPQTEGDAPKTDSVVLLVVYMSLAFGSSLFVFVRSLLVATFGLATAQKLFVKMLRCVFRAPMSFFDTTPSGRILNRVSVDQSVVDLDIAFRLGGFASTTIQLLGIVAVMSKVTWQVLILIVPMAVACMWMQRYYIASSRELTRILSVQKSPVIHLFSESIAGAATIRGFGQEKRFMKRNLYLLDCFARPLFSSLAAIEWLCLRMELLSTFVFAFCMAILVSFPPGTIEPSMAGLAVTYGLNLNARMSRWILSFCKLENRIISVERIYQYCKLPSEAPLIIENSRPSSSWPENGNIELVDLKVRYKDDLPLVLHGISCIFPGGKKIGIVGRTGSGKSTLIQALFRLIEPTGGKVIIDDVDISRIGLHDLRSRLSIIPQDPTLFEGTIRMNLDPLEECTDQEIWEALEKCQLGEVIRSKDEKLDSPVLENGDNWSVGQRQLIALGRALLKQAKILVLDQATASVDTATDNLIQKIIRSEFKDCTVCTIAHRIPTVIDSDLVLVLSDGKIAEFDTPQRLLEDKSSMFMQLVSEYSTRSSCI

Source

organism	Oryza sativa Japonica Group
common_name	Japanese rice
ncbi_taxonomy_id	39947
host_organism	Homo sapiens

Entity 2 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 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	2.630 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.63 Å
resolution_method	—
num_particles	382164

fit	/app/data/saxs_computation/vr/9vrb/9vrb.fit
pddf	/app/data/pr_computation/vr/9vrb/9vrb.pr.out
profile	/app/data/saxs_computation/vr/9vrb/9vrb.dat

Cryo-EM structure of ATP-bound Oryza sativa MRP5 with E1424Q mutation

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