8pfc

;Crystal structure of binary complex between Aster yellows witches'-broom phytoplasma effector SAP05 and the zinc finger domain of SPL5 from Arabidopsis thaliana ;

Method: X-RAY DIFFRACTION D_max: 121.5 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	8pfc
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 zinc finger domain of SPL5 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	37.66 Å
回转半径 Rg (电子) rg_electron	37.13 Å
零角强度 I(0) i0	384617000.00
分子量 molecular_weight	153910.0 kDa
排除体积 excluded_volume	190390 Å³
包络体积 envelope_volume	266380 Å³
水化壳体积 shell_volume	59172 Å³
包络直径 envelope_diameter	125.5 Å
壳层 Rg shell_rg	43.81 Å
包络 Rg envelope_rg	36.49 Å
形状 Rg shape_rg	37.11 Å
总 Rg total_rg	37.62 Å
总原子数 total_atoms	10756
残基数 n_residues	1312
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	121.5 Å
Rg (实空间) rg_real	37.53 Å
Rg 误差 (实空间) rg_real_error	0.97 Å
I(0) (实空间) i0_real	3.8460e+08
I(0) 误差 (实空间) i0_real_error	6.2970e+06
Rg (倒空间) rg_reciprocal	37.61 Å
I(0) (倒空间) i0_reciprocal	384600000.0000
解质量估计 total_estimate	0.8877
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	46.3 Å
偏度 Skewness skewness	0.244
峰度 Kurtosis kurtosis	-0.365
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	28230000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.886

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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 (4)

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	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G,I,K,M,O
原子数 atom_count	11073

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	Squamosa promoter-binding-like protein 5
分子量 formula_weight	8228.5 kDa
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D,F,H,J,L,N,P

GPSRLCQVDRCTVNLTEAKQYYRRHRVCEVHAKASAATVAGVRQRFCQQCSRFHELPEFDEAKRSCRRRL

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 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	20

Entity 4 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	317

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7. 引用文献 (2)

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晶胞边长 a length_a	78.686 Å
晶胞边长 b length_b	165.019 Å
晶胞边长 c length_c	80.862 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	109.65 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	2.200 Å
最低分辨率 resolution_low	74.210 Å
R 因子 r_factor	0.2244
R_work r_work	0.2230
R_free r_free	0.2507

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

;Crystal structure of binary complex between Aster yellows witches'-broom phytoplasma effector SAP05 and the zinc finger domain of SPL5 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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 water

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)