SAXSdb — 9rd8

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1. Structure Basics

entry_id	9rd8
deposition_date	2025-06-02
title	Structure of DabA2B2 complex under 0.1M bicarbonate
keywords	Carbonic anhydrase, Hydro-lyase, Proton-pumping transporter, Carbon-concentrating mechanism, 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	33.91 Å
rg_electron	33.37 Å
i0	305371000.00
molecular_weight	146350.0 kDa
excluded_volume	185550 Å³
envelope_volume	224370 Å³
shell_volume	54192 Å³
envelope_diameter	115.6 Å
shell_rg	41.58 Å
envelope_rg	33.41 Å
shape_rg	33.36 Å
total_rg	34.00 Å
total_atoms	10329
n_residues	1311
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	107.8 Å
rg_real	33.83 Å
rg_real_error	0.75 Å
i0_real	3.0540e+08
i0_real_error	4.8680e+06
rg_reciprocal	33.88 Å
i0_reciprocal	305400000.0000
total_estimate	0.8917
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	41.3 Å
skewness	0.288
kurtosis	-0.359
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	87070000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.874

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Probable inorganic carbon transporter subunit DabA2
formula_weight	95988.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	10329

MTTLTSLQRSEAQRNHIVDLIDKACLRIAPIWPLDSFVAVNPYLGLIDQPFDTVGRYLEQTVGESLFMDHGWFADKIAQGEITDDDLAQAAQQLDPSISLDTIKQQLAVHRQPAPALPLVTNELDRRDAPPVSEFVIEQVSQFMANYYDRGQALWHLPKEASASLFAQWRRYTLINRSASAVGLKQVRQHLLAVPSDAIDALFWALDQINLPESRLPDYLFTLLKTIGGWASWCRYLHFQAGLHGESQHDLRDLLIIRLVWVALVIKETSSAGRQQWRAKLNDWFDPAKLVASPSATATASTKAQSSRIDEILLAAAEQAFRRRINAGLNRQPADAPDQQAERPTVQAAFCIDVRSEVFRRHLEASSPGLETIGFAGFFGLPIDYCRMGESEARLQNPVLINPAYRAQETGDPAIAQHRHARQSRGAIWKQFKLSAASCFTFVESAGLSYVPRLLADSLGWHRSSLPPDAPGLTPEERARLHPQLVKLDGGALSTQEKVDLAEKVLRGLGLTHTFAPIVLLAGHGSSTTNNPHRAGLDCGACAGQAGDVNARVAVQLLNEAAVRLGLIERGIAIPRDTRFVAALHDTTTDHIELLDLDQSGIESDQLSSLTQALKQAGELTRLERLVTLEAQVDTVDAEKQATFRGRDWSQVRPEWGLAGNAAFIAAPRWRTRGLDLGGRAFLHDYDWRHDKEFGVLNVIMTAPLIVANWINLQYYGSTVDNLHQGAGNKVLHNVVGGTVGVIEGNGGDLRVGLAMQSLHDGEQWRHEPLRLSAYIEAPIAEIDKIIAGHDMLNALINNRWMHILHIDDNGIPHRRHAHGDWRPEPISGSLEVLFQGPGGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Source

organism	Halothiobacillus neapolitanus c2
ncbi_taxonomy_id	555778
host_organism	Escherichia coli

Entity 2 polymer

description	Probable inorganic carbon transporter subunit DabB2
formula_weight	59187.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MTIEFSHTTGLLLLAMPALLLMAAVIKPKQGAAYARAYRQRVQWTSFAAFGLALLAVVSFLFARQQNLMLGAGSLPAGLGLLALSIQVNGLTLVLASLVSFVLSVIARYSVQYLDGDPQQARFFRLLAVTGGFFLLVVISGNLGLFTLAIIATGFGLHRLLSFYADRPRAIMATHKKSIFSRTADALLLAATVLIGHQIGSLEFSQISAYVHAQDHLSIALHVAAWLIVLAAILKSAQFPFHGWLIQVMEAPTPVSALMHAGVVYSGAIIVLRTSELLAADGTALLLLALIGLMTLAIGSLVMLTQSAIKSSLAWSTAAQLGFMMLELGLGLFGLALLHLVGHSLYKAHAFLSSGSMTDHLRQAKVLKNRPISVVAWFTTVIVSGLFTLGIAAAMGLSIDQEPMLPAVLTIIALATAQLMLKALSHGTWREILVAAGAAIAMTGVYVFLHEVFITGFADTLAATPQRAPLLDLLLMAITIITFLFVAWLQGPGKTLMSPERQFALFVHLNNGLYLDRWVERLAFRFWPEKVGRAPKKSCAVIPPNPSGIEP

Source

organism	Halothiobacillus neapolitanus c2
ncbi_taxonomy_id	555778
host_organism	Escherichia coli

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	BICARBONATE ION
formula_weight	61.0 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	CARBON DIOXIDE
formula_weight	44.0 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
formula_weight	718.0 kDa
src_method	syn
entity_count	4

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6. Citations (1)

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resolution	3.20 Å
resolution_method	—
num_particles	226711

fit	/app/data/saxs_computation/rd/9rd8/9rd8.fit
pddf	/app/data/pr_computation/rd/9rd8/9rd8.pr.out
profile	/app/data/saxs_computation/rd/9rd8/9rd8.dat

Structure of DabA2B2 complex under 0.1M bicarbonate

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)