SAXSdb — 8s93

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8s93
沉积日期 deposition_date	2023-03-27
结构标题 title	;Crystal structure of the PH-TH/kinase complex of Bruton's tyrosine kinase ;
关键词 keywords	;Bruton's tyrosine kinase, Non-receptor tyrosine kinase, complex, lipid-binding, ATP-binding, TRANSFERASE ;; TRANSFERASE
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	26.76 Å
回转半径 Rg (电子) rg_electron	26.08 Å
零角强度 I(0) i0	41126300.00
分子量 molecular_weight	50169.0 kDa
排除体积 excluded_volume	62969 Å³
包络体积 envelope_volume	77300 Å³
水化壳体积 shell_volume	25579 Å³
包络直径 envelope_diameter	95.1 Å
壳层 Rg shell_rg	32.42 Å
包络 Rg envelope_rg	26.54 Å
形状 Rg shape_rg	26.11 Å
总 Rg total_rg	26.71 Å
总原子数 total_atoms	6973
残基数 n_residues	429
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	93.0 Å
Rg (实空间) rg_real	26.92 Å
Rg 误差 (实空间) rg_real_error	0.84 Å
I(0) (实空间) i0_real	4.1130e+07
I(0) 误差 (实空间) i0_real_error	5.9840e+05
Rg (倒空间) rg_reciprocal	26.88 Å
I(0) (倒空间) i0_reciprocal	41120000.0000
解质量估计 total_estimate	0.8431
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	26.8 Å
偏度 Skewness skewness	0.501
峰度 Kurtosis kurtosis	-0.267
角度范围 angular_range	— – 0.2950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	12520000.0000
实空间数据点数 n_real_points	60
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.752; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.770; Smooth: 0.931

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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	Tyrosine-protein kinase BTK
分子量 formula_weight	52320.7 kDa
EC 编号 ec_number	2.7.10.2
突变 mutation	Q91A, I92A, I94A, I95A, K430R, L542M S543T, V555T, R562K, S564A, P565S, Y617P
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	7273

MAAVILESIFLKRSQQKKKTSPLNFKKRLFLLTVHKLSYYEYDFERGRRGSKKGSIDVEKITCVETVIPEKNPPPERQIPRRGEESSEMEAASAAERFPYPFQVVYDEGPLYVFSPTEELRKRWIHQLKNVIRYNSDLVQKYHPCFWIDGQYLCCSQTAKNAMGCQILENRGGGSGGGGSGGGGSGGGGSGGGEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIRMIREGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGMTRYVLDDEYTSSTGSKFPVKWASPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLPRPHLASERVYTIMYSCWHEKADERPSFKILLSNILDVMDEES

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	;2-[3'-(hydroxymethyl)-1-methyl-5-({5-[(2S)-2-methyl-4-(oxetan-3-yl)piperazin-1-yl]pyridin-2-yl}amino)-6-oxo[1,6-dihydro[3,4'-bipyridine]]-2'-yl]-7,7-dimethyl-3,4,7,8-tetrahydro-2H-cyclopenta[4,5]pyrrolo[1,2-a]pyrazin-1(6H)-one ;
分子量 formula_weight	664.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	1

Entity 4 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	178

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6. 折叠分类 (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

结构域编号 domain_id	8s93A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	29 — PH-domain like
同源超家族 H-superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

结构域编号 domain_id	8s93A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	8s93A03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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7. 引用文献 (1)

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晶胞边长 a length_a	38.376 Å
晶胞边长 b length_b	77.383 Å
晶胞边长 c length_c	82.323 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.98 °
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	monoclinic

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	19.710 Å
R 因子 r_factor	0.2006
R_work r_work	0.1982
R_free r_free	0.2465

fit	/app/data/saxs_computation/s9/8s93/8s93.fit
pddf	/app/data/pr_computation/s9/8s93/8s93.pr.out
profile	/app/data/saxs_computation/s9/8s93/8s93.dat

;Crystal structure of the PH-TH/kinase complex of Bruton's tyrosine kinase ;

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