SAXSdb — 9rd1

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1. Structure Basics

entry_id	9rd1
deposition_date	2025-05-30
title	OppA from E. coli in complex with GSisoK
keywords	;Substrate recognition specificity, Binding pocket plasticity, Transporter-ligand interactions, Structural basis for selective uptake, Scaffold accommodation, TRANSPORT PROTEIN ;; TRANSPORT PROTEIN
method	X-RAY DIFFRACTION

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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	46.92 Å
rg_electron	46.82 Å
i0	1556950000.00
molecular_weight	218450.0 kDa
excluded_volume	211830 Å³
envelope_volume	390780 Å³
shell_volume	70721 Å³
envelope_diameter	155.6 Å
shell_rg	49.95 Å
envelope_rg	45.95 Å
shape_rg	46.83 Å
total_rg	46.91 Å
total_atoms	16596
n_residues	2068
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	158.8 Å
rg_real	46.95 Å
rg_real_error	1.41 Å
i0_real	1.5570e+09
i0_real_error	2.9260e+07
rg_reciprocal	46.92 Å
i0_reciprocal	1557000000.0000
total_estimate	0.8216
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	56.0 Å
skewness	0.265
kurtosis	-0.598
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0001
highest_alpha	76140000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Periplasmic oligopeptide-binding protein OppA
formula_weight	59118.3 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	16697

ADVPAGVTLAEKQTLVRNNGSEVQSLDPHKIEGVPESNISRDLFEGLLVSDLDGHPAPGVAESWDNKDAKVWTFHLRKDAKWSDGTPVTAQDFVYSWQRSVDPNTASPYASYLQYGHIAGIDEILEGKKPITDLGVKAIDDHTLEVTLSEPVPYFYKLLVHPSTSPVPKAAIEKFGEKWTQPGNIVTNGAYTLKDWVVNERIVLERSPTYWNNAKTVINQVTYLPIASEVTDVNRYRSGEIDMTNNSMPIELFQKLKKEIPDEVHVDPYLCTYYYEINNQKPPFNDVRVRTALKLGMDRDIIVNKVKAQGNMPAYGYTPPYTDGAKLTQPEWFGWSQEKRNEEAKKLLAEAGYTADKPLTINLLYNTSDLHKKLAIAASSLWKKNIGVNVKLVNQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSNSSMNTAHYKSPAFDSIMAETLKVTDEAQRTALYTKAEQQLDKDSAIVPVYYYVNARLVKPWVGGYTGKDPLDNTYTRNMYIVKHHHHHH

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 non-polymer

description	Gly-Ser-epsilon-Lys
formula_weight	290.3 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	(R,R)-2,3-BUTANEDIOL
formula_weight	90.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	89

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6. Citations (1)

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length_a	59.990 Å
length_b	200.690 Å
length_c	103.380 Å
angle_alpha	90.00 °
angle_beta	95.73 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.500 Å
resolution_low	30.000 Å
r_factor	0.2314
r_work	0.2294
r_free	0.2593

fit	/app/data/saxs_computation/rd/9rd1/9rd1.fit
pddf	/app/data/pr_computation/rd/9rd1/9rd1.pr.out
profile	/app/data/saxs_computation/rd/9rd1/9rd1.dat

OppA from E. coli in complex with GSisoK

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

Diffraction