SAXSdb — 1opj

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1opj
沉积日期 deposition_date	2003-03-06
结构标题 title	Structural basis for the auto-inhibition of c-Abl tyrosine kinase
关键词 keywords	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	27.97 Å
回转半径 Rg (电子) rg_electron	26.86 Å
零角强度 I(0) i0	71603200.00
分子量 molecular_weight	67832.0 kDa
排除体积 excluded_volume	85480 Å³
包络体积 envelope_volume	105510 Å³
水化壳体积 shell_volume	32763 Å³
包络直径 envelope_diameter	91.5 Å
壳层 Rg shell_rg	34.47 Å
包络 Rg envelope_rg	27.07 Å
形状 Rg shape_rg	26.87 Å
总 Rg total_rg	27.66 Å
总原子数 total_atoms	4770
残基数 n_residues	575
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	87.4 Å
Rg (实空间) rg_real	27.92 Å
Rg 误差 (实空间) rg_real_error	0.55 Å
I(0) (实空间) i0_real	7.1600e+07
I(0) 误差 (实空间) i0_real_error	1.0530e+06
Rg (倒空间) rg_reciprocal	27.94 Å
I(0) (倒空间) i0_reciprocal	71600000.0000
解质量估计 total_estimate	0.9047
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	30.7 Å
偏度 Skewness skewness	0.276
峰度 Kurtosis kurtosis	-0.505
角度范围 angular_range	— – 0.2850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	23140000.0000
实空间数据点数 n_real_points	58
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.926

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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	Proto-oncogene tyrosine-protein kinase ABL1
分子量 formula_weight	33743.5 kDa
EC 编号 ec_number	2.7.1.112
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,B
原子数 atom_count	5001

GAMDPSSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVSAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSISDEVEKELGKRGT

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	Spodoptera frugiperda

Entity 2 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	MYRISTIC ACID
分子量 formula_weight	228.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE
分子量 formula_weight	493.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	231

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1opja1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
家族 Family family	d.144.1.7 — Protein kinases, catalytic subunit

结构域编号 domain_id	d1opja2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1opjb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
家族 Family family	d.144.1.7 — Protein kinases, catalytic subunit

结构域编号 domain_id	d1opjb2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

结构域编号 domain_id	1opjA01
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	1opjA02
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

结构域编号 domain_id	1opjB01
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	1opjB02
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 (2)

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晶胞边长 a length_a	41.844 Å
晶胞边长 b length_b	63.507 Å
晶胞边长 c length_c	64.051 Å
晶胞夹角 α angle_alpha	67.91 °
晶胞夹角 β angle_beta	79.76 °
晶胞夹角 γ angle_gamma	84.88 °
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	1.750 Å
最低分辨率 resolution_low	29.410 Å
R 因子 r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2420

fit	/app/data/saxs_computation/op/1opj/1opj.fit
pddf	/app/data/pr_computation/op/1opj/1opj.pr.out
profile	/app/data/saxs_computation/op/1opj/1opj.dat

Structural basis for the auto-inhibition of c-Abl 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