← Back to search

9y9w

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

Method: X-RAY DIFFRACTION D_max: 161.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9y9w
deposition_date	2025-09-15
title	;Vibrio cholerae protein FrhA peptid-binding domain and adjacent split domain (S1127-F1439) in complex with peptide AGWTD X-ray crystallography structure ;
keywords	Calcium, Adhesin, RTX, peptide-binding domain, split domain, Inhibitor, METAL BINDING PROTEIN; METAL BINDING PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	45.84 Å
rg_electron	45.77 Å
i0	621284000.00
molecular_weight	197060.0 kDa
excluded_volume	242390 Å³
envelope_volume	336810 Å³
shell_volume	62958 Å³
envelope_diameter	169.2 Å
shell_rg	48.80 Å
envelope_rg	44.83 Å
shape_rg	45.74 Å
total_rg	45.98 Å
total_atoms	13827
n_residues	1869
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

▼

3. P(r) Analysis (GNOM)

dmax	161.1 Å
rg_real	46.11 Å
rg_real_error	2.49 Å
i0_real	6.2130e+08
i0_real_error	1.3800e+07
rg_reciprocal	45.85 Å
i0_reciprocal	621100000.0000
total_estimate	0.8532
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	47.4 Å
skewness	0.479
kurtosis	-0.316
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	54910000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.757; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.838

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

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	15182

MASSHHHHHHSSGLVPRGSHMTVIDVDGSQITDSLDVKIVDDASTALDDRGEVDIVADSFTVSGVVANWTSWSNGTNVTTFDGTNAPNGGGLDNDSGKDQIRWGQPASSYSSGYGFIDNDSALNGEFALNQDIILGTFTHYNYPVYSGGAITSASMDVAFSVTDAHGVLTPVTLKLNFDHNETPNTNNPEASKDIIKVGNTNVTFENAGALYTLQVIGFRIPGTNQIVTEIRTGENATNSYELVVRVGPGEGYELPSTSGNVLSNDVSGADVDMTVVGAASGNHVSSGVSGSVGSMIAGLYGNLILLADGSYTYQVTANASSIPNDAIEIFTYTMKDGDGDTSTALLSINVNRVTMADFNANQ

Source

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

Entity 2 polymer

description	Ala-Gly-Trp-Thr-Asp (AGWTD)
formula_weight	548.5 kDa
src_method	syn
entity_count	6

Polymer

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

AGWTD

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	man
entity_count	36

Source

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

Entity 4 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	man
entity_count	5

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1348

▶

6. Citations (2)

▶

length_a	61.273 Å
length_b	118.726 Å
length_c	118.706 Å
angle_alpha	60.03 °
angle_beta	85.62 °
angle_gamma	76.70 °
z_pdb	6

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.400 Å
resolution_low	102.720 Å
r_factor	0.2270
r_work	0.2270
r_free	0.2318

fit	/app/data/saxs_computation/y9/9y9w/9y9w.fit
pddf	/app/data/pr_computation/y9/9y9w/9y9w.pr.out
profile	/app/data/saxs_computation/y9/9y9w/9y9w.dat

;Vibrio cholerae protein FrhA peptid-binding domain and adjacent split domain (S1127-F1439) in complex with peptide AGWTD 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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)