8pq7

;The Potato Late Blight pathogen (Phytophthora infestans) effector protein Pi04134 in complex with potato protein phosphatase type 1c (PP1c). ;

Method: X-RAY DIFFRACTION D_max: 102.1 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	8pq7
沉积日期 deposition_date	2023-07-10
结构标题 title	;The Potato Late Blight pathogen (Phytophthora infestans) effector protein Pi04134 in complex with potato protein phosphatase type 1c (PP1c). ;
关键词 keywords	protein complex, plant pathogen interactions, effector protein, phosphatase, PLANT PROTEIN; PLANT PROTEIN
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	30.11 Å
回转半径 Rg (电子) rg_electron	29.80 Å
零角强度 I(0) i0	106678000.00
分子量 molecular_weight	84106.0 kDa
排除体积 excluded_volume	106150 Å³
包络体积 envelope_volume	127780 Å³
水化壳体积 shell_volume	36156 Å³
包络直径 envelope_diameter	103.6 Å
壳层 Rg shell_rg	36.41 Å
包络 Rg envelope_rg	29.77 Å
形状 Rg shape_rg	29.78 Å
总 Rg total_rg	30.47 Å
总原子数 total_atoms	5905
残基数 n_residues	730
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	102.1 Å
Rg (实空间) rg_real	30.19 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	1.0670e+08
I(0) 误差 (实空间) i0_real_error	1.8800e+06
Rg (倒空间) rg_reciprocal	30.16 Å
I(0) (倒空间) i0_reciprocal	106700000.0000
解质量估计 total_estimate	0.8745
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	30.8 Å
偏度 Skewness skewness	0.430
峰度 Kurtosis kurtosis	-0.299
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	33310000.0000
实空间数据点数 n_real_points	54
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: 0.955; Smooth: 0.943

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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 (5)

Entity 1 polymer

描述 description	Serine/threonine-protein phosphatase
分子量 formula_weight	33600.6 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C
原子数 atom_count	6116

GPMDQNVLDDIITRLLEVKGKPGKQVVLTEAEIKQLCLVAKETFLRQPNLLELEAPIKICGDIHGQYSDLLRLFEYGGLPPQSNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRFNVRLWKIFTDCFNCLPVAALIDEKILCMHGGLSPDLNHLDQIRGLQRPTDVPDAGLLCDLLWSDPSKEVQGWGMNDRGVSYTFGADKVTEFLEKHDLDLICRAHQVVEDGYEFFANRQLVTVFSAPNYCGEFDNAGAMMSVDETLMCSFQILK

来源 Source

来源生物 organism	Solanum tuberosum
通用名 common_name	potato
NCBI 分类编号 ncbi_taxonomy_id	4113
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	RxLR effector protein PexRD24
分子量 formula_weight	10450.2 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

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

GPDLLGLFAKSKLKKMMKSESFKLKRFGEWDDFTVGYIREKLKNKYPDLLLNYLNVYKKAGNEIVRHANNPNKVTFSNKVRARIYKTNS

来源 Source

来源生物 organism	Phytophthora infestans
通用名 common_name	potato late blight agent
NCBI 分类编号 ncbi_taxonomy_id	4787
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 5 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	211

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6. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id	8pq7A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Metallo-dependent phosphatases

结构域编号 domain_id	8pq7C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Metallo-dependent phosphatases

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7. 引用文献 (1)

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晶胞边长 a length_a	55.492 Å
晶胞边长 b length_b	57.036 Å
晶胞边长 c length_c	59.015 Å
晶胞夹角 α angle_alpha	84.35 °
晶胞夹角 β angle_beta	86.49 °
晶胞夹角 γ angle_gamma	89.85 °
晶胞分子数 Z z_pdb	2

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

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	58.620 Å
R 因子 r_factor	0.2048
R_work r_work	0.2025
R_free r_free	0.2514

fit	/app/data/saxs_computation/pq/8pq7/8pq7.fit
pddf	/app/data/pr_computation/pq/8pq7/8pq7.pr.out
profile	/app/data/saxs_computation/pq/8pq7/8pq7.dat

;The Potato Late Blight pathogen (Phytophthora infestans) effector protein Pi04134 in complex with potato protein phosphatase type 1c (PP1c). ;

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 (5)

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 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)