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9rdc

;Crystal structure of Phytophthora infestans effector AVRcap1b in complex with the ENTH domain of Nicotiana benthamiana NbTOL9a protein ;

Method: X-RAY DIFFRACTION D_max: 180.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rdc
deposition_date	2025-06-02
title	;Crystal structure of Phytophthora infestans effector AVRcap1b in complex with the ENTH domain of Nicotiana benthamiana NbTOL9a protein ;
keywords	Plant pathology, vesicle trafficking, ESCRT, plant immunity, PROTEIN BINDING; PROTEIN BINDING
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	51.70 Å
rg_electron	52.02 Å
i0	391534000.00
molecular_weight	167770.0 kDa
excluded_volume	212230 Å³
envelope_volume	348560 Å³
shell_volume	61412 Å³
envelope_diameter	179.4 Å
shell_rg	48.47 Å
envelope_rg	50.99 Å
shape_rg	52.00 Å
total_rg	51.92 Å
total_atoms	11839
n_residues	1470
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	180.9 Å
rg_real	51.98 Å
rg_real_error	2.41 Å
i0_real	3.9150e+08
i0_real_error	8.1420e+06
rg_reciprocal	51.45 Å
i0_reciprocal	391200000.0000
total_estimate	0.5512
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	54.3 Å
skewness	0.467
kurtosis	-0.399
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	15940000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.723; Stabil: 1.000; Sysdev: 0.007; Positv: 1.000; Valcen: 0.973; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	RxLR effector protein PITG_16705
formula_weight	70519.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	11839

GPAPSIVENIKALVKSSAVTPAKLQQWLDERLPAGLVFKNMNLDEPNIFSLLHEPNFAKWVQYADDLSAKSSHKESSVISTLTSLHGDKVVYDTIQAAKLYPQLSELALKLEKDQIRFWIATRKDPSVVFEALNLNWAGISIFPKPEFSAWLKYVDDVNARHPKEAPLSIIPTLKQRFSRGDEAGTDVLLKLIANGKATTEAKTVANKVESALFDFWLNSRETPDKVMDAFKYGTTTQAFLGSPRWKEWERYLSAYNARYPEKKATAIETLTRKYGDAQLLDTLIGASSKGETKTLAAKLQAQQFDRWMNLKESPLDVYNRLRSSYGDTAFFNEPQLNVWVSYMNVFVDKNPSKVDKMFLELGDTFGDMRLFRVLGEAKKFPNLESTATKLQMEKASTLFASGKSPEGIFKVLALDNVGDDILSNTLFHKWLAYLQKFNKEHPNNQESWFDMLRISYQPFGVERIIETGRKNPLTRLMAEKVENAYHNYWLDIKMEPKTAFRSLHLDESGEKLLADPKFNTWVQYLKTFNDRYPNEKTTVIDGLRDNSHDIALLRMFSAAKNDPSTEKLATDLQSALILKWQDAKKTPEELKRVFVGVPAADEMLDRYIKLLAVASSTP

Source

organism	Phytophthora infestans
common_name	potato late blight agent
ncbi_taxonomy_id	4787
host_organism	Escherichia coli

Entity 2 polymer

description	Target of myb protein 1
formula_weight	16936.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

GPMVNSMVERATSDMLIGPDWAMNIEICDICNHDPAQAKDVVKGIKRRLGSKNPKVQLLALTLLETIVKNCGDIVHMHVAEKDLLHEMVKIVKKKQPDLHVKEKVLILIDTWQEAFGGPRARYPQFYGAYQELLRIGAVFPQRSERSAPV

Source

organism	Nicotiana benthamiana
ncbi_taxonomy_id	4100
host_organism	Escherichia coli

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6. Citations (2)

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length_a	85.874 Å
length_b	136.912 Å
length_c	195.574 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	4.100 Å
resolution_low	79.570 Å
r_factor	0.2500
r_work	0.2482
r_free	0.2860

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

;Crystal structure of Phytophthora infestans effector AVRcap1b in complex with the ENTH domain of Nicotiana benthamiana NbTOL9a protein ;

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)