SAXSdb — 9rvx

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1. Structure Basics

entry_id	9rvx
deposition_date	2025-07-09
last_revision	2026-05-20
title	Structure of CrtA with citrate
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	37.53 Å
rg_electron	37.36 Å
i0	369014000.00
molecular_weight	150130.0 kDa
excluded_volume	185260 Å³
envelope_volume	237450 Å³
shell_volume	52712 Å³
envelope_diameter	130.0 Å
shell_rg	43.72 Å
envelope_rg	37.03 Å
shape_rg	37.36 Å
total_rg	37.73 Å
total_atoms	10623
n_residues	1376
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	124.7 Å
rg_real	37.59 Å
rg_real_error	1.38 Å
i0_real	3.6900e+08
i0_real_error	7.0450e+06
rg_reciprocal	37.56 Å
i0_reciprocal	369000000.0000
total_estimate	0.8744
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	38.6 Å
skewness	0.356
kurtosis	-0.526
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	95810000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.890

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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	10727

MKQTSLYYATLGLVGLALAAPARAQEQSLPVQLAPVVVHGAPEANGPLNLDAVDSTGSRLGLTLRETPASVTVINREQIEARGALDTQEIARGIVGVDNASPPGSAGSVSYRGFSGSQVSQLFNGISVQYDVVAARPIDSWIYDRVEAIGGPSSFLFGAGAVGGAINYVTKVAQRDTFYDGQLRLGSYGARQASVGLNRQLAGEPGGRGQYLRIDANANASDGWVDGNRSHAEQVAASLLSDLGERVTHTLALEYQHEMVHRPYWGTPLTTDGDGVVRGEGHIRGGTRWKNYNVDDGRYEQSVWWLRSLTEWQASDRLSFRNTLYYYRADRDFQNLETYRYNPGNSQVLRSGALLQRHEQRLLGNRIEGLYHGSLGGLRSDWSFGADYSVNRQTRYPTSVAGQVDSVDPYEFDPGEFYDIPGMRRGHVPDRDNKVRTLAFMLENRTEVGGGVALVTALRHDIIDLDLTNRRAASAASPGHASRRYNPTTGRVAVNWEVSPGATLYAQYATAADPPSGVLSTATFADVLNNDKLTTGTQVEAGGKFAFWDGRGTATVAVYEIKRKNLATPDPLNPGSSLPVGSQSARGLELAGGLQLTRALSLQANLALVDPRYDDFSQNVGGVAVSRNGKVPVNTPRRLANVWLDYAFAPDWRASLAARHVGKTYADAANTVWAPAYTVFDAALSHRIDRHFSVTARVRNLTDKVYAASVTGAPMYYLGAPRSVELALQARF

Source

organism	Bordetella pertussis
ncbi_taxonomy_id	520
host_organism	Escherichia coli

Entity 2 non-polymer

description	CITRATE ANION
formula_weight	189.1 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	104

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6. Citations (1)

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length_a	67.143 Å
length_b	67.900 Å
length_c	102.518 Å
angle_alpha	89.27 °
angle_beta	80.30 °
angle_gamma	68.56 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.295 Å
resolution_low	26.000 Å
r_factor	0.2353
r_work	0.2335
r_free	0.2722

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

Structure of CrtA with citrate

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