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9tan

Local refinement of E. coli Complex I D79N NuoA mutant hydrophilic domain in LMNG

Method: ELECTRON MICROSCOPY D_max: 142.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tan
deposition_date	2025-11-18
title	Local refinement of E. coli Complex I D79N NuoA mutant hydrophilic domain in LMNG
keywords	;PROTON TRANSPORT, bioenergetics, Leigh's syndrome ;; PROTON TRANSPORT
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	43.37 Å
rg_electron	43.47 Å
i0	1174980000.00
molecular_weight	277540.0 kDa
excluded_volume	344070 Å³
envelope_volume	429500 Å³
shell_volume	79699 Å³
envelope_diameter	151.0 Å
shell_rg	50.09 Å
envelope_rg	43.84 Å
shape_rg	43.56 Å
total_rg	43.43 Å
total_atoms	19382
n_residues	2449
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	142.0 Å
rg_real	43.33 Å
rg_real_error	0.98 Å
i0_real	1.1750e+09
i0_real_error	1.9880e+07
rg_reciprocal	43.37 Å
i0_reciprocal	1175000000.0000
total_estimate	0.8868
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	47.3 Å
skewness	0.308
kurtosis	-0.447
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0001
highest_alpha	280200000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.833

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	NADH-quinone oxidoreductase subunit B
formula_weight	25081.8 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	19678

MDYTLTRIDPNGENDRYPLQKQEIVTDPLEQEVNKNVFMGKLNDMVNWGRKNSIWPYNFGLSCCYVEMVTSFTAVHDVARFGAEVLRASPRQADLMVVAGTCFTKMAPVIQRLYDQMLEPKWVISMGACANSGGMYDIYSVVQGVDKFIPVDVYIPGCPPRPEAYMQALMLLQESIGKERRPLSWVVGDQGVYRANMQSERERKRGERIAVTNLRTPDEI

Source

organism	Escherichia coli BW25113
ncbi_taxonomy_id	679895
host_organism	Escherichia coli BW25113

Entity 2 polymer

description	NADH-quinone oxidoreductase subunit C/D
formula_weight	68780.5 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MVNNMTDLTAQEPAWQTRDHLDDPVIGELRNRFGPDAFTVQATRTGVPVVWIKREQLLEVGDFLKKLPKPYVMLFDLHGMDERLRTHREGLPAADFSVFYHLISIDRNRDIMLKVALAENDLHVPTFTKLFPNANWYERETWDLFGITFDGHPNLRRIMMPQTWKGHPLRKDYPARATEFSPFELTKAKQDLEMEALTFKPEEWGMKRGTENEDFMFLNLGPNHPSAHGAFRIVLQLDGEEIVDCVPDIGYHHRGAEKMGERQSWHSYIPYTDRIEYLGGCVNEMPYVLAVEKLAGITVPDRVNVIRVMLSELFRINSHLLYISTFIQDVGAMTPVFFAFTDRQKIYDLVEAITGFRMHPAWFRIGGVAHDLPRGWDRLLREFLDWMPKRLASYEKAALQNTILKGRSQGVAAYGAKEALEWGTTGAGLRATGIDFDVRKARPYSGYENFDFEIPVGGGVSDCYTRVMLKVEELRQSLRILEQCLNNMPEGPFKADHPLTTPPPKERTLQHIETLITHFLQVSWGPVMPANESFQMIEATKGINSYYLTSDGSTMSYRTRVRTPSFAHLQQIPAAIRGSLVSDLIVYLGSIDFVMSDVDR

Source

organism	Escherichia coli BW25113
ncbi_taxonomy_id	679895
host_organism	Escherichia coli BW25113

Entity 3 polymer

description	NADH-quinone oxidoreductase subunit E
formula_weight	18614.0 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MHENQQPQTEAFELSAAEREAIEHEMHHYEDPRAASIEALKIVQKQRGWVPDGAIHAIADVLGIPASDVEGVATFYSQIFRQPVGRHVIRYCDSVVCHINGYQGIQAALEKKLNIKPGQTTFDGRFTLLPTCCLGNCDKGPNMMIDEDTHAHLTPEAIPELLERYK

Source

organism	Escherichia coli BW25113
ncbi_taxonomy_id	679895
host_organism	Escherichia coli BW25113

Entity 4 polymer

description	NADH-quinone oxidoreductase subunit F
formula_weight	51208.4 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MRGSHHHHHHTDPALRAKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEIVNQVKDAGLKGRGGAGFSTGLKWSLMPKDESMNIRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAAVNLRRAIAEATEAGLLGKNIMGTGFDFELFVHTGAGRYICGEETALINSLEGRRANPRSKPPFPATSGAWGKPTCVNNVETLCNVPAILANGVEWYQNISKSKDAGTKLMGFSGRVKNPGLWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFLTEAHLDLPMEFESIGKAGSRLGTALAMAVDHEINMVSLVRNLEEFFARESCGWCTPCRDGLPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAHAPGAVEPLQSAIKYFREEFEAGIKQPFSNTHLINGIQPNLLKERW

Source

organism	Escherichia coli BW25113
ncbi_taxonomy_id	679895
host_organism	Escherichia coli BW25113

Entity 5 polymer

description	NADH-quinone oxidoreductase subunit G
formula_weight	100663.6 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MLMATIHVDGKEYEVNGADNLLEACLSLGLDIPYFCWHPALGSVGACRQCAVKQYQNAEDTRGRLVMSCMTPASDGTFISIDDEEAKQFRESVVEWLMTNHPHDCPVCEEGGNCHLQDMTVMTGHSFRRYRFTKRTHRNQDLGPFISHEMNRCIACYRCVRYYKDYADGTDLGVYGAHDNVYFGRPEDGTLESEFSGNLVEICPTGVFTDKTHSERYNRKWDMQFAPSICQQCSIGCNISPGERYGELRRIENRYNGTVNHYFLCDRGRFGYGYVNLKDRPRQPVQRRGDDFITLNAEQAMQGAADILRQSKKVIGIGSPRASVESNFALRELVGEENFYTGIAHGEQERLQLALKVLREGGIYTPALREIESYDAVLVLGEDVTQTGARVALAVRQAVKGKAREMAAAQKVADWQIAAILNIGQRAKHPLFVTNVDDTRLDDIAAWTYRAPVEDQARLGFAIAHALDNSAPAVDGIEPELQSKIDVIVQALAGAKKPLIISGTNAGSLEVIQAAANVAKALKGRGADVGITMIARSVNSMGLGIMGGGSLEEALTELETGRADAVVVLENDLHRHASAIRVNAALAKAPLVMVVDHQRTAIMENAHLVLSAASFAESDGTVINNEGRAQRFFQVYDPAYYDSKTVMLESWRWLHSLHSTLLSREVDWTQLDHVIDAVVAKIPELAGIKDAAPDATFRIRGQKLAREPHRYSGRTAMRANISVHEPRQPQDIDTMFTFSMEGNNQPTAHRSQVPFAWAPGWNSPQAWNKFQDEVGGKLRFGDPGVRLFETSENGLDYFTSVPARFQPQDGKWRIAPYYHLFGSDELSQRAPVFQSRMPQPYIKLNPADAAKLGVNAGTRVSFSYDGNTVTLPVEIAEGLTAGQVGLPMGMSGIAPVLAGAHLEDLKEAQQ

Source

organism	Escherichia coli BW25113
ncbi_taxonomy_id	679895
host_organism	Escherichia coli BW25113

Entity 6 polymer

description	NADH-quinone oxidoreductase subunit I
formula_weight	20562.8 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

MTLKELLVGFGTQVRSIWMIGLHAFAKRETRMYPEEPVYLPPRYRGRIVLTRDPDGEERCVACNLCAVACPVGCISLQKAETKDGRWYPEFFRINFSRCIFCGLCEEACPTTAIQLTPDFEMGEYKRQDLVYEKEDLLISGPGKYPEYNFYRMAGMAIDGKDKGEAENEAKPIDVKSLLP

Source

organism	Escherichia coli BW25113
ncbi_taxonomy_id	679895
host_organism	Escherichia coli BW25113

Entity 7 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	7

Entity 8 non-polymer

description	FE2/S2 (INORGANIC) CLUSTER
formula_weight	175.8 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	4

Entity 10 non-polymer

description	FLAVIN MONONUCLEOTIDE
formula_weight	456.3 kDa
src_method	syn
entity_count	1

Entity 11 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	296

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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	2.59 Å
resolution_method	—
num_particles	86927

fit	/app/data/saxs_computation/ta/9tan/9tan.fit
pddf	/app/data/pr_computation/ta/9tan/9tan.pr.out
profile	/app/data/saxs_computation/ta/9tan/9tan.dat

Local refinement of E. coli Complex I D79N NuoA mutant hydrophilic domain in LMNG

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 (11)

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 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)