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9ybq

;Vibrio cholerae protein FrhA peptid-binding domain and adjacent split domain (S1127-F1439) in complex with peptide AGYTD X-ray crystallography structure ;

Method: X-RAY DIFFRACTION D_max: 151.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ybq
deposition_date	2025-09-17
title	;Vibrio cholerae protein FrhA peptid-binding domain and adjacent split domain (S1127-F1439) in complex with peptide AGYTD X-ray crystallography structure ;
keywords	Calcium, Adhesin, RTX, peptide-binding domain, split domain, Inhibitor, METAL BINDING PROTEIN; METAL BINDING 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	47.01 Å
rg_electron	46.86 Å
i0	636932000.00
molecular_weight	198750.0 kDa
excluded_volume	244500 Å³
envelope_volume	372090 Å³
shell_volume	69837 Å³
envelope_diameter	147.9 Å
shell_rg	47.94 Å
envelope_rg	46.00 Å
shape_rg	46.87 Å
total_rg	46.90 Å
total_atoms	26926
n_residues	1895
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	151.5 Å
rg_real	47.06 Å
rg_real_error	1.25 Å
i0_real	6.3690e+08
i0_real_error	1.2870e+07
rg_reciprocal	47.01 Å
i0_reciprocal	636900000.0000
total_estimate	0.8168
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	53.5 Å
skewness	0.343
kurtosis	-0.436
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	28540000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Cadherin domain protein
formula_weight	38041.1 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,E,G,I,K
atom_count	28638

MASSHHHHHHSSGLVPRGSHMTVIDVDGSQITDSLDVKIVDDASTALDDRGEVDIVADSFTVSGVVANWTSWSNGTNVTTFDGTNAPNGGGLDNDSGKDQIRWGQPASSYSSGYGFIDNDSALNGEFALNQDIILGTFTHYNYPVYSGGAITSASMDVAFSVTDAHGVLTPVTLKLNFDHNETPNTNNPEASKDIIKVGNTNVTFENAGALYTLQVIGFRIPGTNQIVTEIRTGENATNSYELVVRVGPGEGYELPSTSGNVLSNDVSGADVDMTVVGAASGNHVSSGVSGSVGSMIAGLYGNLILLADGSYTYQVTANASSIPNDAIEIFTYTMKDGDGDTSTALLSINVNRVTMADFNANQ

Source

organism	Vibrio cholerae O395
ncbi_taxonomy_id	345073
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	ALA-GLY-TYR-THR-ASP
formula_weight	525.5 kDa
src_method	syn
entity_count	6

Polymer

type	polypeptide(L)
strand_id	M,N,O,P,Q,R

AGYTD

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	man
entity_count	36

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1712

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6. Citations (2)

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length_a	61.394 Å
length_b	118.717 Å
length_c	118.728 Å
angle_alpha	60.05 °
angle_beta	76.45 °
angle_gamma	81.42 °
z_pdb	6

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.500 Å
resolution_low	59.180 Å
r_factor	0.2480
r_work	0.2479
r_free	0.2518

fit	/app/data/saxs_computation/yb/9ybq/9ybq.fit
pddf	/app/data/pr_computation/yb/9ybq/9ybq.pr.out
profile	/app/data/saxs_computation/yb/9ybq/9ybq.dat

;Vibrio cholerae protein FrhA peptid-binding domain and adjacent split domain (S1127-F1439) in complex with peptide AGYTD X-ray crystallography structure ;

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

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)