2b8t

Crystal structure of Thymidine Kinase from U.urealyticum in complex with thymidine

Method: X-RAY DIFFRACTION D_max: 83.3 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	2b8t
沉积日期 deposition_date	2005-10-10
结构标题 title	Crystal structure of Thymidine Kinase from U.urealyticum in complex with thymidine
关键词 keywords	DEOXYRIBONUCLEOSIDE KINASE, ZINC-BINDING DOMAIN, TK1, UU-TK, THYMIDINE, 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	28.45 Å
回转半径 Rg (电子) rg_electron	27.03 Å
零角强度 I(0) i0	132045000.00
分子量 molecular_weight	91782.0 kDa
排除体积 excluded_volume	115400 Å³
包络体积 envelope_volume	142720 Å³
水化壳体积 shell_volume	41684 Å³
包络直径 envelope_diameter	86.8 Å
壳层 Rg shell_rg	36.27 Å
包络 Rg envelope_rg	27.14 Å
形状 Rg shape_rg	27.05 Å
总 Rg total_rg	27.91 Å
总原子数 total_atoms	6460
残基数 n_residues	798
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	83.3 Å
Rg (实空间) rg_real	28.18 Å
Rg 误差 (实空间) rg_real_error	0.13 Å
I(0) (实空间) i0_real	1.2740e+08
I(0) 误差 (实空间) i0_real_error	1.4290e+06
Rg (倒空间) rg_reciprocal	28.27 Å
I(0) (倒空间) i0_reciprocal	132100000.0000
解质量估计 total_estimate	0.7255
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	38.7 Å
偏度 Skewness skewness	0.078
峰度 Kurtosis kurtosis	-0.462
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	6.2980
最高正则化参数 α highest_alpha	53850000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 0.914; Sysdev: 0.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.888

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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	Thymidine kinase
分子量 formula_weight	25440.2 kDa
EC 编号 ec_number	2.7.1.21
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	6690

MAKVNAFSKKIGWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFFKNKKRNKNI

来源 Source

来源生物 organism	Ureaplasma parvum
NCBI 分类编号 ncbi_taxonomy_id	134821
宿主生物 host_organism	Escherichia coli

Entity 2 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	4

Entity 3 non-polymer

描述 description	THYMIDINE
分子量 formula_weight	242.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
分子量 formula_weight	122.1 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	230

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2b8ta1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.24 — Type II thymidine kinase

结构域编号 domain_id	d2b8ta2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
超家族 Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
家族 Family family	g.39.1.14 — Type II thymidine kinase zinc finger

结构域编号 domain_id	d2b8tb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.24 — Type II thymidine kinase

结构域编号 domain_id	d2b8tb2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
超家族 Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
家族 Family family	g.39.1.14 — Type II thymidine kinase zinc finger

结构域编号 domain_id	d2b8tc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.24 — Type II thymidine kinase

结构域编号 domain_id	d2b8tc2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
超家族 Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
家族 Family family	g.39.1.14 — Type II thymidine kinase zinc finger

结构域编号 domain_id	d2b8td1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.24 — Type II thymidine kinase

结构域编号 domain_id	d2b8td2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
超家族 Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
家族 Family family	g.39.1.14 — Type II thymidine kinase zinc finger

CATH v4.4 (8 domains)

结构域编号 domain_id	2b8tA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	2b8tA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2b8tB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	2b8tB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2b8tC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	2b8tC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2b8tD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	2b8tD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	20 —

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7. 引用文献 (1)

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晶胞边长 a length_a	57.158 Å
晶胞边长 b length_b	115.649 Å
晶胞边长 c length_c	64.474 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	101.02 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	26.950 Å
R 因子 r_factor	0.1974
R_work r_work	0.1953
R_free r_free	0.2350

fit	/app/data/saxs_computation/b8/2b8t/2b8t.fit
pddf	/app/data/pr_computation/b8/2b8t/2b8t.pr.out
profile	/app/data/saxs_computation/b8/2b8t/2b8t.dat