8gmb

;Crystal structure of the full-length Bruton's tyrosine kinase (PH-TH domain not visible) ;

Method: X-RAY DIFFRACTION D_max: 131.4 Å Quality: REASONABLE

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	8gmb
沉积日期 deposition_date	2023-03-24
结构标题 title	;Crystal structure of the full-length Bruton's tyrosine kinase (PH-TH domain not visible) ;
关键词 keywords	ATP-binding, Lipid-binding, transcription regulation, immunity, 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	36.49 Å
回转半径 Rg (电子) rg_electron	36.88 Å
零角强度 I(0) i0	34668300.00
分子量 molecular_weight	44783.0 kDa
排除体积 excluded_volume	55127 Å³
包络体积 envelope_volume	87912 Å³
水化壳体积 shell_volume	22667 Å³
包络直径 envelope_diameter	126.6 Å
壳层 Rg shell_rg	37.40 Å
包络 Rg envelope_rg	36.78 Å
形状 Rg shape_rg	36.96 Å
总 Rg total_rg	36.64 Å
总原子数 total_atoms	5661
残基数 n_residues	438
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	131.4 Å
Rg (实空间) rg_real	37.29 Å
Rg 误差 (实空间) rg_real_error	1.83 Å
I(0) (实空间) i0_real	3.4670e+07
I(0) 误差 (实空间) i0_real_error	6.1940e+05
Rg (倒空间) rg_reciprocal	36.80 Å
I(0) (倒空间) i0_reciprocal	34650000.0000
解质量估计 total_estimate	0.6521
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	24.4 Å
偏度 Skewness skewness	0.582
峰度 Kurtosis kurtosis	-0.725
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3003000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.163; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.032; Smooth: 0.952

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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 (2)

Entity 1 polymer

描述 description	Tyrosine-protein kinase BTK
分子量 formula_weight	76400.3 kDa
EC 编号 ec_number	2.7.10.2
突变 mutation	E298A, K300A, E301A, A384P, S386P, T387P, A388P, L390F, 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	5661

MAAVILESIFLKRSQQKKKTSPLNFKKRLFLLTVHKLSYYEYDFERGRRGSKKGSIDVEKITCVETVIPEKNPPPERQIPRRGEESSEMEQISIIERFPYPFQVVYDEGPLYVFSPTEELRKRWIHQLKNVIRYNSDLVQKYHPCFWIDGQYLCCSQTAKNAMGCQILENRNGSLKPGSSHRKTKKPLPPTPEEDQILKKPLPPEPTAAPISTTELKKVVALYDYMPMNANDLQLRKGEEYFILEESNLPWWRARDKNGQEGYIPSNYITEAEDSIEMYEWYSKHMTRSQAEQLLKQAGAAGGFIVRDSSKAGKYTVSVFAKSTGEPQGVIRHYVVCSTPQSQYYLAEKHLFSTIPELINYHQHNSAGLISRLKYPVSKQNKNPPPPPGFGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIRMIREGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGMTRYVLDDEYTSSTGSKFPVKWASPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLPRPHLASERVYTIMYSCWHEKADERPSFKILLSNILDVMDEES

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

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7. 引用文献 (1)

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晶胞边长 a length_a	125.718 Å
晶胞边长 b length_b	125.718 Å
晶胞边长 c length_c	110.091 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	120.00 °
晶胞分子数 Z z_pdb	6

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	trigonal

分辨率 resolution	3.400 Å
最低分辨率 resolution_low	19.940 Å
R 因子 r_factor	0.2727
R_work r_work	0.2719
R_free r_free	0.2891

fit	/app/data/saxs_computation/gm/8gmb/8gmb.fit
pddf	/app/data/pr_computation/gm/8gmb/8gmb.pr.out
profile	/app/data/saxs_computation/gm/8gmb/8gmb.dat

;Crystal structure of the full-length Bruton's tyrosine kinase (PH-TH domain not visible) ;

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)