SAXSdb — 9j5k

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9j5k
沉积日期 deposition_date	2024-08-12
结构标题 title	Pathogen effector forms a phosphatase holoenzyme complex with host core enzyme to promote disease
关键词 keywords	pathogen; PP2A core enzyme; virulent function; susceptibility, PLANT PROTEIN; PLANT PROTEIN
实验方法 method	ELECTRON MICROSCOPY

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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	69.60 Å
回转半径 Rg (电子) rg_electron	69.67 Å
零角强度 I(0) i0	1050900000.00
分子量 molecular_weight	270080.0 kDa
排除体积 excluded_volume	336320 Å³
包络体积 envelope_volume	555320 Å³
水化壳体积 shell_volume	69487 Å³
包络直径 envelope_diameter	216.5 Å
壳层 Rg shell_rg	62.05 Å
包络 Rg envelope_rg	68.35 Å
形状 Rg shape_rg	69.68 Å
总 Rg total_rg	69.46 Å
总原子数 total_atoms	19056
残基数 n_residues	2698
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	203.8 Å
Rg (实空间) rg_real	69.95 Å
Rg 误差 (实空间) rg_real_error	1.59 Å
I(0) (实空间) i0_real	1.0510e+09
I(0) 误差 (实空间) i0_real_error	2.1720e+07
Rg (倒空间) rg_reciprocal	68.05 Å
I(0) (倒空间) i0_reciprocal	1047000000.0000
解质量估计 total_estimate	0.8190
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	55.6 Å
偏度 Skewness skewness	0.365
峰度 Kurtosis kurtosis	-0.832
角度范围 angular_range	— – 0.1100 Å⁻¹
当前正则化参数 α current_alpha	0.0011
最高正则化参数 α highest_alpha	33890000.0000
实空间数据点数 n_real_points	23
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.829; 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 (5)

Entity 1 polymer

描述 description	Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
分子量 formula_weight	35635.2 kDa
EC 编号 ec_number	3.1.3.16
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	C,F
原子数 atom_count	19056

MDEKVFTKELDQWIEQLNECKQLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFRIGGKSPDTNYLFMGDYVNRGYYSVETVTLLVALKVRYRERITILRGNHESRQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSFLQFDPAPRRGEPHVTRRTPDYFL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 2 polymer

描述 description	RxLR effector protein PSR2
分子量 formula_weight	74706.7 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,E

MRLQCVVLFAALTLVAATHAPPNVKTVLSAEQHDIPVKRLLRPGNPAGKEDEERGINFSSVPGFEKLANLLKPKPGLKKLLKWADAKKPPETVFTRLRLDKTGTQLFDNTDFPVWAAYTRSVAQTDSEASAVMLKTLVSRYSDEVLSGMIAAAKKSSKTESIATKLETEQMRTWLAAKKTPDDMFLVFKLNKAGDDILSSPLLSAWTNYMKLSNKENPKAQTTLIATMTKHYGDSGVSQILAAARKSPATQSTAKRLEAEQVQLWLKKGRTPDDTFTLLSLDRAGDDLLASPQFNTWMKYINYYNKENPDEKTTVLAKLMTHFDDEELTPILVVARKVPSTESTAAKLQAEQFKNWLSADKSPEEAFTLLQLDKAGDDLLTNPQLTNWLKYTENFNLNKEINEQVTAIQVFRAQYVDDSRIANMVIAAEKVPNTQAIAKRVEDELFKGWTVVLNKPDDVFINLKLETVGENVFESPLWSFYTKFLEKYNTANPGKEQTMISGLARGYNDVTLTNMLLKAKEAPSTKTLATKLEDELVQYWLADKKLPDKLFGYLELKESVDGILTNPVFNVWLKYLNAFNDKAPVKKALMIDTLKSAFGDVAVSNMLFAAKKDPGTAKVAATLQTALLSKWVLEKKTPGQVSAILKEGAGADVSAKLLATYSAKFKVRWG

来源 Source

来源生物 organism	Phytophthora sojae
NCBI 分类编号 ncbi_taxonomy_id	67593
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform
分子量 formula_weight	65667.0 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,D

MSMIDEPLYPIAVLIDELKNDDIQLRLNSIRRLSTIARALGEERTRKELIPFLSENNDDDDEVLLAMAEELGVFIPYVGGVEYAHVLLPPLETLSTVEETCVREKAVESLCRVGSQMRESDLVDHFISLVKRLAAGEWFTARVSACGVFHIAYPSAPDMLKTELRSLYTQLCQDDMPMVRRAAATNLGKFAATVESAHLKTDVMSMFEDLTQDDQDSVRLLAVEGCAALGKLLEPQDCVQHILPVIVNFSQDKSWRVRYMVANQLYELCEAVGPEPTRTELVPAYVRLLRDNEAEVRIAAAGKVTKFCRILNPEIAIQHILPCVKELSSDSSQHVRSALASVIMGMAPVLGKDATIEHLLPIFLSLLKDEFPDVRLNIISKLDQVNQVIGIDLLSQSLLPAIVELAEDRHWRVRLAIIEYIPLLASQLGVGFFDDKLGALCMQWLQDKVHSIRDAAANNLKRLAEEFGPEWAMQHIVPQVLEMVNNPHYLYRMTILRAVSLLAPVMGSEITCSKLLPVVMTASKDRVPNIKFNVAKVLQSLIPIVDQSVVEKTIRPGLVELSEDPDVDVRFFANQALQSIDNVMMSS

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

Entity 4 polymer

描述 description	random substrate
分子量 formula_weight	754.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	X,Y

RRATVA

Entity 5 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

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7. 引用文献 (1)

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分辨率 resolution	3.39 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	156653

fit	/app/data/saxs_computation/j5/9j5k/9j5k.fit
pddf	/app/data/pr_computation/j5/9j5k/9j5k.pr.out
profile	/app/data/saxs_computation/j5/9j5k/9j5k.dat

Pathogen effector forms a phosphatase holoenzyme complex with host core enzyme to promote disease

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

冷冻电镜 EM 3D

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 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

Entity 5 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)