SAXSdb — 9rvq

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1. Structure Basics

entry_id	9rvq
deposition_date	2025-07-08
last_revision	2026-05-20
title	Structure of CrtA with betaOG
keywords	TBDT, TonB dependet transporter, copper, 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	37.61 Å
rg_electron	37.41 Å
i0	370405000.00
molecular_weight	150960.0 kDa
excluded_volume	186540 Å³
envelope_volume	239650 Å³
shell_volume	53007 Å³
envelope_diameter	132.0 Å
shell_rg	43.83 Å
envelope_rg	37.13 Å
shape_rg	37.41 Å
total_rg	37.77 Å
total_atoms	10680
n_residues	1382
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	126.6 Å
rg_real	37.67 Å
rg_real_error	1.10 Å
i0_real	3.7040e+08
i0_real_error	6.3810e+06
rg_reciprocal	37.64 Å
i0_reciprocal	370400000.0000
total_estimate	0.8716
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	39.2 Å
skewness	0.358
kurtosis	-0.514
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	94670000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.913

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	TonB-dependent receptor
formula_weight	79460.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	11296

MKQTSLYYATLGLVGLALAAPARAQEQSLPVQLAPVVVHGAPEANGPLNLDAVDSTGSRLGLTLRETPASVTVINREQIEARGALDTQEIARGIVGVDNASPPGSAGSVSYRGFSGSQVSQLFNGISVQYDVVAARPIDSWIYDRVEAIGGPSSFLFGAGAVGGAINYVTKVAQRDTFYDGQLRLGSYGARQASVGLNRQLAGEPGGRGQYLRIDANANASDGWVDGNRSHAEQVAASLLSDLGERVTHTLALEYQHEMVHRPYWGTPLTTDGDGVVRGEGHIRGGTRWKNYNVDDGRYEQSVWWLRSLTEWQASDRLSFRNTLYYYRADRDFQNLETYRYNPGNSQVLRSGALLQRHEQRLLGNRIEGLYHGSLGGLRSDWSFGADYSVNRQTRYPTSVAGQVDSVDPYEFDPGEFYDIPGMRRGHVPDRDNKVRTLAFMLENRTEVGGGVALVTALRHDIIDLDLTNRRAASAASPGHASRRYNPTTGRVAVNWEVSPGATLYAQYATAADPPSGVLSTATFADVLNNDKLTTGTQVEAGGKFAFWDGRGTATVAVYEIKRKNLATPDPLNPGSSLPVGSQSARGLELAGGLQLTRALSLQANLALVDPRYDDFSQNVGGVAVSRNGKVPVNTPRRLANVWLDYAFAPDWRASLAARHVGKTYADAANTVWAPAYTVFDAALSHRIDRHFSVTARVRNLTDKVYAASVTGAPMYYLGAPRSVELALQARF

Source

organism	Bordetella pertussis
ncbi_taxonomy_id	520
host_organism	Escherichia coli

Entity 2 non-polymer

description	octyl beta-D-glucopyranoside
formula_weight	292.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	467

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6. Citations (1)

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length_a	68.103 Å
length_b	120.081 Å
length_c	119.550 Å
angle_alpha	90.00 °
angle_beta	102.24 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.075 Å
resolution_low	116.830 Å
r_factor	0.2502
r_work	0.2474
r_free	0.3030

fit	/app/data/saxs_computation/rv/9rvq/9rvq.fit
pddf	/app/data/pr_computation/rv/9rvq/9rvq.pr.out
profile	/app/data/saxs_computation/rv/9rvq/9rvq.dat

Structure of CrtA with betaOG

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