8pfd

;Crystal structure of binary complex between Aster yellows witches'-broom phytoplasma effector SAP05 and the von Willebrand Factor Type A domain of the proteasomal ubiquitin receptor Rpn10 from Arabidopsis thaliana ;

Method: X-RAY DIFFRACTION D_max: 68.0 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8pfd
沉积日期 deposition_date	2023-06-15
结构标题 title	;Crystal structure of binary complex between Aster yellows witches'-broom phytoplasma effector SAP05 and the von Willebrand Factor Type A domain of the proteasomal ubiquitin receptor Rpn10 from Arabidopsis thaliana ;
关键词 keywords	Targeted protein degradation, ubiquitin-independent, bacterial effector protein, 26S proteasome, PROTEIN BINDING; PROTEIN BINDING
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	20.75 Å
回转半径 Rg (电子) rg_electron	19.83 Å
零角强度 I(0) i0	16836900.00
分子量 molecular_weight	31271.0 kDa
排除体积 excluded_volume	39302 Å³
包络体积 envelope_volume	45934 Å³
水化壳体积 shell_volume	19797 Å³
包络直径 envelope_diameter	69.9 Å
壳层 Rg shell_rg	25.79 Å
包络 Rg envelope_rg	19.99 Å
形状 Rg shape_rg	19.85 Å
总 Rg total_rg	20.60 Å
总原子数 total_atoms	2200
残基数 n_residues	285
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	68.0 Å
Rg (实空间) rg_real	20.74 Å
Rg 误差 (实空间) rg_real_error	0.44 Å
I(0) (实空间) i0_real	1.6840e+07
I(0) 误差 (实空间) i0_real_error	2.1820e+05
Rg (倒空间) rg_reciprocal	20.75 Å
I(0) (倒空间) i0_reciprocal	16840000.0000
解质量估计 total_estimate	0.8051
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	24.7 Å
偏度 Skewness skewness	0.370
峰度 Kurtosis kurtosis	-0.258
角度范围 angular_range	— – 0.3850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3612000.0000
实空间数据点数 n_real_points	70
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	Sequence-variable mosaic (SVM) signal sequence domain-containing protein
分子量 formula_weight	12310.9 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	2230

GPAPNEEFVGDMRIVNVNLSNIDILKKHETFKKYFDFTLTGPRYNGNIAEFAMIWKIKNPPLNLLGVFFDDGTRDDEDDKYILEELKQIGNGAKNMYIFWQYEQK

来源 Source

来源生物 organism	;Aster yellows witches'-broom phytoplasma AYWB ;
NCBI 分类编号 ncbi_taxonomy_id	322098
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	26S proteasome non-ATPase regulatory subunit 4 homolog
分子量 formula_weight	20879.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

GPVLEATMICIDNSEWMRNGDYSPSRLQAQTEAVNLLCGAKTQSNPENTVGILTMAGKGVRVLTTPTSDLGKILACMHGLDVGGEINLTAAIQIAQLALKHRQNKNQRQRIIVFAGSPIKYEKKALEIVGKRLKKNSVSLDIVNFGEDDDEEKPQKLEALLTAVNNNDGSHIVHVPSGANALSDVLLSTPVFTG

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	thale cress
NCBI 分类编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	30

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7. 引用文献 (2)

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晶胞边长 a length_a	42.391 Å
晶胞边长 b length_b	68.599 Å
晶胞边长 c length_c	49.851 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	92.78 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.170 Å
最低分辨率 resolution_low	49.840 Å
R 因子 r_factor	0.2004
R_work r_work	0.1979
R_free r_free	0.2522

fit	/app/data/saxs_computation/pf/8pfd/8pfd.fit
pddf	/app/data/pr_computation/pf/8pfd/8pfd.pr.out
profile	/app/data/saxs_computation/pf/8pfd/8pfd.dat

;Crystal structure of binary complex between Aster yellows witches'-broom phytoplasma effector SAP05 and the von Willebrand Factor Type A domain of the proteasomal ubiquitin receptor Rpn10 from Arabidopsis thaliana ;

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 water

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)