SAXSdb — 8yl6

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8yl6
沉积日期 deposition_date	2024-03-05
结构标题 title	EDS1-SAG101-NRG1A L134E heterotrimer
关键词 keywords	;Effector-triggered immunity (ETI), Enhanced Disease Susceptibility1, Senescence-Associated Gene101, N Required Gene 1.1, IMMUNE SYSTEM, IMMUNE SYSTEM-HYDROLASE complex ;; IMMUNE SYSTEM/HYDROLASE
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	39.71 Å
回转半径 Rg (电子) rg_electron	39.60 Å
零角强度 I(0) i0	674111000.00
分子量 molecular_weight	140450.0 kDa
排除体积 excluded_volume	135460 Å³
包络体积 envelope_volume	264460 Å³
水化壳体积 shell_volume	56469 Å³
包络直径 envelope_diameter	136.4 Å
壳层 Rg shell_rg	44.45 Å
包络 Rg envelope_rg	39.12 Å
形状 Rg shape_rg	39.63 Å
总 Rg total_rg	39.74 Å
总原子数 total_atoms	10632
残基数 n_residues	1439
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	134.6 Å
Rg (实空间) rg_real	39.76 Å
Rg 误差 (实空间) rg_real_error	1.32 Å
I(0) (实空间) i0_real	6.7410e+08
I(0) 误差 (实空间) i0_real_error	1.0890e+07
Rg (倒空间) rg_reciprocal	39.73 Å
I(0) (倒空间) i0_reciprocal	674100000.0000
解质量估计 total_estimate	0.8775
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	50.5 Å
偏度 Skewness skewness	0.356
峰度 Kurtosis kurtosis	-0.335
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	129900000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.851; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.871

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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	Protein EDS1
分子量 formula_weight	71784.2 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	10632

MAFEALTGINGDLITRSWSASKQAYLTERYHKEEAGAVVIFAFQPSFSEKDFFDPDNKSSFGEIKLNRVQFPCMRKIGKGDVATVNEAFLKNLEAIIDPRTSFQASVEMAVRSRKQIVFTGHSSGGATAILATVWYLEKYFIRNPNVYLEPRCVTFGAPLVGDSIFSHALGREKWSRFFVNFVSRFDIVPRIMLARKASVEETLPHVLAQLDPRKSSVQESEQRITEFYTRVMRDTSTVANQAVCELTGSAEAFLETLSSFLELSPYRPAGTFVFSTEKRLVAVNNSDAILQMLFYTSQASDEQEWSLIPFRSIRDHHSYEELVQSMGKKLFNHLDGENSIESTLNDLGVSTRGRQYVQAALEEEKKRVENQKKIIQVIEQERFLKKLAWIEDEYKPKCQAHKNGYYDSFKVSNEENDFKANVKRAELAGVFDEVLGLMKKCQLPDEFEGDIDWIKLATRYRRLVEPLDIANYHRHLKNEDTGPYMKRGRPTRYIYAQRGYEHYILKPNGMIAEDVFWNKVNGLNLGLQLEEIQETLKNSGSECGSCFWAEVEELKGKPYEEVEVRVKTLEGMLGEWITDGEVDDKEIFLEGSTFRKWWITLPKNHKSHSPLRDYMMDEITDT

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	Arabidopsis thaliana

Entity 2 polymer

描述 description	Senescence-associated carboxylesterase 101
分子量 formula_weight	62153.4 kDa
EC 编号 ec_number	3.1.1.1
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

MESSSSLKGSALGKLVVTSGLLHSSWSKILEIHNPPYSNHDPGLQVSKKKKDSGLEFQIHREEKFTLVVFSAPPICRSSSSDSTLLHVKDKENPFPFLCSENNPSFSLHTPAFNLFTSASTSLTYLKSELLQTLKSEKPVIITGAALGGSVASLYTLWLLETIEPTLKRPLCITFGSPLIGDASLQQILENSVRNSCFLHVVSAQTRIKMDFFKPFGTFLICFDSGCVCIEDHVAVTELLNGVHDSGLVDYSQVLNRLDQSMLSLADSRLIPEDVIKGIEKRAEMKNLRFDMMFKKLNDMKISMAYIEWYKKKCKEVKIGYYDRFKTQLAFPSKEFDINIKNHHKSELNRFWKSVVEEVERRPQSDASILKRRFLFSGNNYRRMIEPLDIAEYYLEGRKEYRTTGRSHHYVMLEKWFGMESILIEKERCKKRDLSDLLTFDSCFWAEVEDSLIVINQLNTTVGMRDDVREVLTRKLVEFEGYVWEIITKREVSPEIFLEESSFMKWWKEYKKIKGFNSSYLTEFMNTRKYESYGKSQ

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	Arabidopsis thaliana

Entity 3 polymer

描述 description	Probable disease resistance protein At5g66900
分子量 formula_weight	92368.7 kDa
突变 mutation	L134E
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	C

MNDWASLGIGSIGEAVFSKLLKVVIDEAKKFKAFKPLSKDLVSTMEILFPLTQKIDSMQKELDFGVKELKELRDTIERADVAVRKFPRVKWYEKSKYTRKIERINKDMLKFCQIDLQLLQHRNQLTLLGLTGNEVNSVDGLSKRMDLLSVPAPVFRDLCSVPKLDKVIVGLDWPLGELKKRLLDDSVVTLVVSAPPGCGKTTLVSRLCDDPDIKGKFKHIFFNVVSNTPNFRVIVQNLLQHNGYNALTFENDSQAEVGLRKLLEELKENGPILLVLDDVWRGADSFLQKFQIKLPNYKILVTSRFDFPSFDSNYRLKPLEDDDARALLIHWASRPCNTSPDEYEDLLQKILKRCNGFPIVIEVVGVSLKGRSLNTWKGQVESWSEGEKILGKPYPTVLECLQPSFDALDPNLKECFLDMGSFLEDQKIRASVIIDMWVELYGKGSSILYMYLEDLASQNLLKLVPLGTNEHEDGFYNDFLVTQHDILRELAICQSEFKENLERKRLNLEILENTFPDWCLNTINASLLSISTDDLFSSKWLEMDCPNVEALVLNLSSSDYALPSFISGMKKLKVLTITNHGFYPARLSNFSCLSSLPNLKRIRLEKVSITLLDIPQLQLSSLKKLSLVMCSFGEVFYDTEDIVVSNALSKLQEIDIDYCYDLDELPYWISEIVSLKTLSITNCNKLSQLPEAIGNLSRLEVLRLCSSMNLSELPEATEGLSNLRFLDISHCLGLRKLPQEIGKLQNLKKISMRKCSGCELPESVTNLENLEVKCDEETGLLWERLKPKMRNLRVQEEEIEHNLNLLQMF

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	Arabidopsis thaliana

Entity 4 non-polymer

描述 description	;[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-[(2~{S},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate ;
分子量 formula_weight	1048.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	—

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

分辨率 resolution	3.10 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	142555

fit	/app/data/saxs_computation/yl/8yl6/8yl6.fit
pddf	/app/data/pr_computation/yl/8yl6/8yl6.pr.out
profile	/app/data/saxs_computation/yl/8yl6/8yl6.dat

EDS1-SAG101-NRG1A L134E heterotrimer

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

冷冻电镜 EM 3D

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 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)